MESSAGE
| DATE | 2020-03-25 |
| FROM | From: "Pat Schloss"
|
| SUBJECT | Subject: [Hangout - NYLXS] [mothur] mothur v.1.44.0
|
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Subject: [Hangout - NYLXS] [mothur] mothur v.1.44.0
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Hello mothur users,
We are happy to announce the release of mothur v.1.44.0 m/mothur/mothur/releases/latest>! There are a number of other things to te=
ll you about that coincide with this release.
First, in this release we have a number of new commands, feature enhanceme=
nts, and bug fixes. To help foster reproducibility, we have created the sra=
.info command, which will help you to d=
ownload sequence data from the SRA and prepare it for analysis with the typ=
ical mothur pipelines. We have also added the make.clr wiki/make.clr/> command, which applies the centered log-ratio transformatio=
n of OTU abundance data. This is a popular approach to accounting for the c=
ompositional nature of microbiome sequence data. Although mothur=E2=80=99s =
pre.cluster is arguably one of the f=
irst methods of assigning sequences to amplicon/exact sequence variants, we=
never made it super easy to go from a count table file to a shared file. A=
lthough I still have some reservations about ASV/ESVs, with this release ma=
ke.shared will take a count table an=
d create a shared and list file for you. This is demonstrated in the MiSeq =
SOP . Finally, for those of you that ar=
e fans of the batch mode feature in m=
othur, we have added a number of new features to improve their utility incl=
uding the ability to use your operating system=E2=80=99s environment variab=
les.
Second, December marked the 10th anniversary of the publishing of the pape=
r describing mothur . This spring, =
AEM published a retrospective mini-review /e02343-19> of mothur's development and the lesson's we've learned over the=
past 10 years. Even though it focuses on mothur, I think the lessons are g=
enerally valuable. We are grateful to all the past and current mothur users=
that have helped to shape mothur.
Third, if you've been to the mothur website you'=
ll noticed that it has received a major rework. We had been experiencing so=
me hosting and general security problems over the years that recently escal=
ated. It has been transformed to a Jekyll-based wiki that is written in mar=
kdown hosted on G=
itHub. You=E2=80=99ll also notice that the formulae for the calculators now=
render correctly. Please let us know if you see a problem with any of the =
documentation by clicking on the GitHub link on the page. This would also b=
e an excellent time to get your own GitHub account if you don't have one al=
ready!
Fourth, like many of you, we are adjusting to a new way of trying to do sc=
ience. There are more important things going on in the world right now than=
finding the best way to analyze sequence data. That being said, if you hav=
e the mental and time bandwidth, I would encourage you to check out our fre=
e resources for learning to program and make your data analyses more reprod=
ucible. Over the years, I've developed an extensive R tutorial riffomonas.org/minimalR/> for analyzing mothur output and a series of lesso=
ns on reproducible research h/>. Starting Thursday afternoon, I will be hosting an activity that has be=
en successful in my lab called Code Club ub/>, which is an interactive way to help people develop and strengthen the=
ir programming skills. It is designed to serve people of all skill levels a=
nd will involve working with data from diverse sources. Next week, I will s=
tart to live stream a dat=
a analysis project that I will run through YouTube. I welcome your particip=
ation during the stream. To keep things light during this time stressful ti=
me, I will re-analyze and expand upon Five Thirty Eight=E2=80=99s question =
-know-is-her-name/> of whether we can predict someone=E2=80=99s age from th=
eir name. If you=E2=80=99re interested in the live stream idea, please leav=
e a comment on the page describing the project live_streams/2020-04-01-guessing-age-from-a-name> telling me when and how o=
ften you=E2=80=99d like to see something. All of these activities will be r=
ecorded and posted to YouTube for you to watch later if you can't join us. =
Please spread the word about these activities to your personal and virtual =
social networks.
As always, thank you for your support of mothur.
Take care of yourselves!
Pat
Enhancements:
Adds sra.info command to download and extract samples from NCBI using pref=
etch and fasterq-dump written by NCBI. #27 r/issues/27>
Adds make.clr command. #695
Adds clr file type to metastats command. #695 othur/issues/695>
Expands batch files. #601 #6=
58
Adds environment variables to mothur. #601 ur/issues/601>
Adds MOTHUR_TOOLS option to allow you to set the location of mothur's exte=
rnal tools at compile time or through the set.dir command at run time. #682=
Adds uchime parameter to chimera.uchime. #682 othur/issues/682>
Adds vsearch parameter to chimera.vsearch, cluster, cluster.split commands=
. #682
Improves mothur's checkorient option in make.contigs. Also sets checkorien=
t=3Dt by default.
split.abund command 's cutoff parameter can now be a percentage. Removes f=
asta file requirement. #263
Adds contigsreport to get.seqs and remove.seqs commands. #660 hub.com/mothur/mothur/issues/660>
Adds processors option to split.groups. #685 thur/issues/685>
Adds sets to remove.groups and get.groups commands. #277 om/mothur/mothur/issues/277>
Adds parallelization to chimera.vsearch when using denovo method. #700 tps://github.com/mothur/mothur/issues/700>
Changes filter.seqs fasta file delimantor from '-' to '|' to allow for '-'=
's in filenames.
Adds list file output for make.shared with count table.
Bugs:
Fixes tree.shared distance being used instead of similarity.
Fixes bug with remove.seqs not removing empty groups from the count table.=
#675
Fixes bug with trim.seqs if no name file is given and allfiles=3DT. #696 <=
https://github.com/mothur/mothur/issues/696>
Fixes corr.axes bug when metadata files contain zeroed columns.
-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-
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charset=utf-8
=
=3Dutf-8">space; line-break: after-white-space;" class=3D"">=3D"word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-whi= te-space;" class=3D""> bkit-nbsp-mode: space; line-break: after-white-space;" class=3D""> =3D"auto" style=3D"word-wrap: break-word; -webkit-nbsp-mode: space; line-b= reak: after-white-space;" class=3D""> break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class= = =3D""> rgb(36, 41, 46); font-size: 14px;" class=3D"">Hello mothur users,iv> color: rgb(36, 41, 46);" class=3D"">
: 14px;" class=3D"">We are happy to announce the release of pan>le=3D"font-size: 14px;" class=3D"">mothur v.1.44.0! 2e" class=3D"">an style=3D"font-size: 14px;" class=3D""> There are a number of other=
things to tell you about that coincide with this release.
span>
First, in t=
his release we have a number of new commands, feature enhancements, and bug=
fixes. To help foster reproducibility, we have created the pan>othur.org/wiki/sra.info/" class=3D"">sra.infoass=3D""> com=
mand, which will help you to download sequence data from the SRA and prepar=
e it for analysis with the typical mothur pipelines. We have also added the=
">make.clr command, which appli=
es the centered log-ratio transformation of OTU abundance data. This is a p=
opular approach to accounting for the compositional nature of microbiome se=
quence data. Although mothur=E2=80=99s r.org/wiki/pre.cluster/" class=3D"">pre.clusterclass=3D""> is arguably one of the first methods of assigning sequence=
s to amplicon/exact sequence variants, we never made it super easy to go fr=
om a count table file to a shared file. Although I still have some reservat=
ions about ASV/ESVs, with this release r.org/wiki/make.shared/" class=3D"">make.sharedclass=3D""> will take a count table and create a shared and list file =
for you. This is demonstrated in the org/wiki/miseq_sop/" class=3D"">MiSeq SOP=3D"">. Finally, for those of you that are fans of the =
=3D"https://mothur.org/wiki/batch_mode/" class=3D"">batch mode<= font color=3D"#24292e" class=3D""> ""> feature in mothur, we have added a number of new features to impro=
ve their utility including the ability to use your operating system=E2=80=
=99s environment variables.
e=3D"font-size: 14px; caret-color: rgb(36, 41, 46);" class=3D"">Second, Dec=
ember marked the 10th anniversary of the publishing of the nt> 4px;" class=3D"">paper describing mothur=3D"font-size: 14px;" class=3D"">6);" class=3D"">. This spring, AEM published a ref=3D"https://aem.asm.org/content/86/2/e02343-19" style=3D"font-size: 14px=
;" class=3D"">retrospective mini-review"">"> of mothur's development and the lesson's we've learned over the pas=
t 10 years. Even though it focuses on mothur, I think the lessons are =
generally valuable. We are grateful to all the past and current mothur user=
s that have helped to shape mothur.
nt style=3D"caret-color: rgb(36, 41, 46); font-size: 14px;" class=3D"">Thir=
d, if you've been to the " class=3D"">mothur website<=
/a>1, 46);" class=3D""> you'll noticed that it has received a major rewor=
k. We had been experiencing some hosting and general security problems=
over the years that recently escalated. It has been transformed to a Jekyl=
l-based wiki that is written in s.github.com/features/mastering-markdown/" class=3D"">markdownont color=3D"#24292e" class=3D"">"> hosted on GitHub. You=E2=80=99ll also notice that=
the formulae for the calculators now render correctly. Please let us know =
if you see a problem with any of the documentation by clicking on the =
GitHub link on the page. This would also be an excellent time to get your o=
wn GitHub account if you don't have one already!
=
e: 14px;" class=3D"">Fourth, like many of you, we are adjusting to a new wa=
y of trying to do science. There are more important things going on in the =
world right now than finding the best way to analyze sequence data. Th=
at being said, if you have the mental and time bandwidth, I would encourage=
you to check out our free resources for learning to program and make =
your data analyses more reproducible. Over the years, I've developed an&nbs=
p;://www.riffomonas.org/minimalR/" class=3D"">extensive R tutorialolor=3D"#24292e" class=3D"">lass=3D""> for analyzing mothur output and a series of lessons on=
rch/" class=3D"">reproducible research">. Starting Thurs=
day afternoon, I will be hosting an activity that has been successful in my=
lab called ub/" class=3D"">Code Club=
=3D"caret-color: rgb(36, 41, 46);" class=3D"">, which is an interacti=
ve way to help people develop and strengthen their programming skills. It i=
s designed to serve people of all skill levels and will involve working wit=
h data from diverse sources. Next week, I will start to =
live=
stream a data=
analysis project that I will run through YouTube. I welcome your participa=
tion during the stream. To keep things light during this time stressful tim=
e, I will re-analyze and expand upon fivethirtyeight.com/features/how-to-tell-someones-age-when-all-you-know-is-=
her-name/" class=3D"">Five Thirty Eight=E2=80=99s question=3D"#24292e" class=3D""> of whether we can predict s=
omeone=E2=80=99s age from their name. If you=E2=80=99re interested in the l=
ive stream idea, please leave a comment on the =3D"https://www.riffomonas.org/live_streams/2020-04-01-guessing-age-from-a=
-name" class=3D"">page describing the project92e" class=3D"">"> telling me when and how often you=E2=80=99d like to see something. =
All of these activities will be recorded and posted to YouTube for you=
to watch later if you can't join us. Please spread the word about these ac=
tivities to your personal and virtual social networks.
>
41, 46);" class=3D"">As always, thank you for your support of mothur.t>
: rgb(36, 41, 46);" class=3D"">Take care of yourselves!
">>Pat
nt>b(36, 41, 46); color: rgb(36, 41, 46); margin-top: 0px !important;" class=
=3D"">Enhancements: =
rgin-bottom: 16px; caret-color: rgb(36, 41, 46); color: rgb(36, 41, 46);" c=
lass=3D"">- ont-size: 14px;" class=3D"">Adds sra=
.info command to download and extract samples from NCBI using prefetch =
and fasterq-dump written by NCBI. " data-error-text=3D"Failed to load title" data-id=3D"54935575" data-permis=
sion-text=3D"Title is private" data-url=3D"https://github.com/mothur/mothur=
/issues/27" data-hovercard-type=3D"issue" data-hovercard-url=3D"/mothur/mot=
hur/issues/27/hovercard" href=3D"https://github.com/mothur/mothur/issues/27=
" style=3D"box-sizing: border-box; color: rgb(3, 102, 214); text-decoration=
: none;">#27 - : 0.25em;" class=3D"">Adds make=
.clr command. "Failed to load title" data-id=3D"550904296" data-permission-text=3D"Title =
is private" data-url=3D"https://github.com/mothur/mothur/issues/695" data-h=
overcard-type=3D"issue" data-hovercard-url=3D"/mothur/mothur/issues/695/hov=
ercard" href=3D"https://github.com/mothur/mothur/issues/695" style=3D"box-s=
izing: border-box; color: rgb(3, 102, 214); text-decoration: none;">#695> - s=3D"">Adds clr file type to me=
tastats command. =
=3D"Failed to load title" data-id=3D"550904296" data-permission-text=3D"Ti=
tle is private" data-url=3D"https://github.com/mothur/mothur/issues/695" da=
ta-hovercard-type=3D"issue" data-hovercard-url=3D"/mothur/mothur/issues/695=
/hovercard" href=3D"https://github.com/mothur/mothur/issues/695" style=3D"b=
ox-sizing: border-box; color: rgb(3, 102, 214); text-decoration: none;">#69=
5 - class=3D"">Expands batch files.=
ad title" data-id=3D"429824073" data-permission-text=3D"Title is private" d=
ata-url=3D"https://github.com/mothur/mothur/issues/601" data-hovercard-type=
=
=3D"issue" data-hovercard-url=3D"/mothur/mothur/issues/601/hovercard" href=
=
=3D"https://github.com/mothur/mothur/issues/601" style=3D"box-sizing: bord=
er-box; color: rgb(3, 102, 214); text-decoration: none;">#601 lass=3D"issue-link js-issue-link" data-error-text=3D"Failed to load title" =
data-id=3D"495784845" data-permission-text=3D"Title is private" data-url=3D=
"https://github.com/mothur/mothur/issues/658" data-hovercard-type=3D"issue"=
data-hovercard-url=3D"/mothur/mothur/issues/658/hovercard" href=3D"https:/=
/github.com/mothur/mothur/issues/658" style=3D"box-sizing: border-box; colo=
r: rgb(3, 102, 214); text-decoration: none;">#658 - =3D"box-sizing: border-box; margin-top: 0.25em;" class=3D"">"font-size: 14px;" class=3D"">Adds environment variables to mothur. class=3D"issue-link js-issue-link" data-error-text=3D"Failed to load title=
" data-id=3D"429824073" data-permission-text=3D"Title is private" data-url=
=3D"https://github.com/mothur/mothur/issues/601" data-hovercard-type=3D"is=
sue" data-hovercard-url=3D"/mothur/mothur/issues/601/hovercard" href=3D"htt=
ps://github.com/mothur/mothur/issues/601" style=3D"box-sizing: border-box; =
color: rgb(3, 102, 214); text-decoration: none;">#601 - yle=3D"box-sizing: border-box; margin-top: 0.25em;" class=3D"">=3D"font-size: 14px;" class=3D"">Adds MOTHUR_TOOLS option to allow you to =
set the location of mothur's external tools at compile time or through the =
set.dir command at run time. a-error-text=3D"Failed to load title" data-id=3D"516141179" data-permission=
-text=3D"Title is private" data-url=3D"https://github.com/mothur/mothur/iss=
ues/682" data-hovercard-type=3D"issue" data-hovercard-url=3D"/mothur/mothur=
/issues/682/hovercard" href=3D"https://github.com/mothur/mothur/issues/682"=
style=3D"box-sizing: border-box; color: rgb(3, 102, 214); text-decoration:=
none;">#682 - : 0.25em;" class=3D"">Adds uchi=
me parameter to chimera.uchime. data-error-text=3D"Failed to load title" data-id=3D"516141179" data-permiss=
ion-text=3D"Title is private" data-url=3D"https://github.com/mothur/mothur/=
issues/682" data-hovercard-type=3D"issue" data-hovercard-url=3D"/mothur/mot=
hur/issues/682/hovercard" href=3D"https://github.com/mothur/mothur/issues/6=
82" style=3D"box-sizing: border-box; color: rgb(3, 102, 214); text-decorati=
on: none;">#682 - top: 0.25em;" class=3D"">Adds v=
search parameter to chimera.vsearch, cluster, cluster.split commands. =
le" data-id=3D"516141179" data-permission-text=3D"Title is private" data-ur=
l=3D"https://github.com/mothur/mothur/issues/682" data-hovercard-type=3D"is=
sue" data-hovercard-url=3D"/mothur/mothur/issues/682/hovercard" href=3D"htt=
ps://github.com/mothur/mothur/issues/682" style=3D"box-sizing: border-box; =
color: rgb(3, 102, 214); text-decoration: none;">#682 - yle=3D"box-sizing: border-box; margin-top: 0.25em;" class=3D"">=3D"font-size: 14px;" class=3D"">Improves mothur's checkorient option in m=
ake.contigs. Also sets checkorient=3Dt by default. - box-sizing: border-box; margin-top: 0.25em;" class=3D"">-size: 14px;" class=3D"">split.abund command 's cutoff parameter can now be=
a percentage. Removes fasta file requirement. js-issue-link" data-error-text=3D"Failed to load title" data-id=3D"17013367=
6" data-permission-text=3D"Title is private" data-url=3D"https://github.com=
/mothur/mothur/issues/263" data-hovercard-type=3D"issue" data-hovercard-url=
=
=3D"/mothur/mothur/issues/263/hovercard" href=3D"https://github.com/mothur=
/mothur/issues/263" style=3D"box-sizing: border-box; color: rgb(3, 102, 214=
); text-decoration: none;">#263 - der-box; margin-top: 0.25em;" class=3D"">lass=3D"">Adds contigsreport to get.seqs and remove.seqs commands. class=3D"issue-link js-issue-link" data-error-text=3D"Failed to load title"=
data-id=3D"495958028" data-permission-text=3D"Title is private" data-url=
=3D"https://github.com/mothur/mothur/issues/660" data-hovercard-type=3D"is=
sue" data-hovercard-url=3D"/mothur/mothur/issues/660/hovercard" href=3D"htt=
ps://github.com/mothur/mothur/issues/660" style=3D"box-sizing: border-box; =
color: rgb(3, 102, 214); text-decoration: none;">#660 - yle=3D"box-sizing: border-box; margin-top: 0.25em;" class=3D"">=3D"font-size: 14px;" class=3D"">Adds processors option to split.groups.&n=
bsp; title" data-id=3D"519290805" data-permission-text=3D"Title is private" dat=
a-url=3D"https://github.com/mothur/mothur/issues/685" data-hovercard-type=
=3D"issue" data-hovercard-url=3D"/mothur/mothur/issues/685/hovercard" href=
=
=3D"https://github.com/mothur/mothur/issues/685" style=3D"box-sizing: bord=
er-box; color: rgb(3, 102, 214); text-decoration: none;">#685i> - n style=3D"font-size: 14px;" class=3D"">Adds sets to remove.groups and get.=
groups commands. =
=3D"Failed to load title" data-id=3D"180643897" data-permission-text=3D"Ti=
tle is private" data-url=3D"https://github.com/mothur/mothur/issues/277" da=
ta-hovercard-type=3D"issue" data-hovercard-url=3D"/mothur/mothur/issues/277=
/hovercard" href=3D"https://github.com/mothur/mothur/issues/277" style=3D"b=
ox-sizing: border-box; color: rgb(3, 102, 214); text-decoration: none;">#27=
7 - class=3D"">Adds parallelization=
to chimera.vsearch when using denovo method. s-issue-link" data-error-text=3D"Failed to load title" data-id=3D"564140410=
" data-permission-text=3D"Title is private" data-url=3D"https://github.com/=
mothur/mothur/issues/700" data-hovercard-type=3D"issue" data-hovercard-url=
=3D"/mothur/mothur/issues/700/hovercard" href=3D"https://github.com/mothur=
/mothur/issues/700" style=3D"box-sizing: border-box; color: rgb(3, 102, 214=
); text-decoration: none;">#700 - der-box; margin-top: 0.25em;" class=3D"">lass=3D"">Changes filter.seqs fasta file delimantor from '-' to '|' to allo=
w for '-''s in filenames. - argin-top: 0.25em;" class=3D"">=
Adds list file output for make.shared with count table. style=3D"box-sizing: border-box; margin-top: 0px; margin-bottom: 16px; care=
t-color: rgb(36, 41, 46); color: rgb(36, 41, 46);" class=3D"">=3D"font-size: 14px;" class=3D"">Bugs: > _._,_._,_
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_._,_._,_ --Apple-Mail=_BEF47628-6B45-4443-A66F-D079A56B0801-- --===============1123175537== Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Content-Disposition: inline _______________________________________________ Hangout mailing list Hangout-at-nylxs.com http://lists.mrbrklyn.com/mailman/listinfo/hangout --===============1123175537==-- --===============1123175537== Content-Type: multipart/alternative; boundary="Apple-Mail=_BEF47628-6B45-4443-A66F-D079A56B0801" --Apple-Mail=_BEF47628-6B45-4443-A66F-D079A56B0801 Content-Transfer-Encoding: quoted-printable Content-Type: text/plain; charset=utf-8 Hello mothur users, We are happy to announce the release of mothur v.1.44.0 m/mothur/mothur/releases/latest>! There are a number of other things to te=
ll you about that coincide with this release.
First, in this release we have a number of new commands, feature enhanceme=
nts, and bug fixes. To help foster reproducibility, we have created the sra=
.info command, which will help you to d=
ownload sequence data from the SRA and prepare it for analysis with the typ=
ical mothur pipelines. We have also added the make.clr wiki/make.clr/> command, which applies the centered log-ratio transformatio=
n of OTU abundance data. This is a popular approach to accounting for the c=
ompositional nature of microbiome sequence data. Although mothur=E2=80=99s =
pre.cluster is arguably one of the f=
irst methods of assigning sequences to amplicon/exact sequence variants, we=
never made it super easy to go from a count table file to a shared file. A=
lthough I still have some reservations about ASV/ESVs, with this release ma=
ke.shared will take a count table an=
d create a shared and list file for you. This is demonstrated in the MiSeq =
SOP . Finally, for those of you that ar=
e fans of the batch mode feature in m=
othur, we have added a number of new features to improve their utility incl=
uding the ability to use your operating system=E2=80=99s environment variab=
les.
Second, December marked the 10th anniversary of the publishing of the pape=
r describing mothur . This spring, =
AEM published a retrospective mini-review /e02343-19> of mothur's development and the lesson's we've learned over the=
past 10 years. Even though it focuses on mothur, I think the lessons are g=
enerally valuable. We are grateful to all the past and current mothur users=
that have helped to shape mothur.
Third, if you've been to the mothur website you'=
ll noticed that it has received a major rework. We had been experiencing so=
me hosting and general security problems over the years that recently escal=
ated. It has been transformed to a Jekyll-based wiki that is written in mar=
kdown hosted on G=
itHub. You=E2=80=99ll also notice that the formulae for the calculators now=
render correctly. Please let us know if you see a problem with any of the =
documentation by clicking on the GitHub link on the page. This would also b=
e an excellent time to get your own GitHub account if you don't have one al=
ready!
Fourth, like many of you, we are adjusting to a new way of trying to do sc=
ience. There are more important things going on in the world right now than=
finding the best way to analyze sequence data. That being said, if you hav=
e the mental and time bandwidth, I would encourage you to check out our fre=
e resources for learning to program and make your data analyses more reprod=
ucible. Over the years, I've developed an extensive R tutorial riffomonas.org/minimalR/> for analyzing mothur output and a series of lesso=
ns on reproducible research h/>. Starting Thursday afternoon, I will be hosting an activity that has be=
en successful in my lab called Code Club ub/>, which is an interactive way to help people develop and strengthen the=
ir programming skills. It is designed to serve people of all skill levels a=
nd will involve working with data from diverse sources. Next week, I will s=
tart to live stream a dat=
a analysis project that I will run through YouTube. I welcome your particip=
ation during the stream. To keep things light during this time stressful ti=
me, I will re-analyze and expand upon Five Thirty Eight=E2=80=99s question =
-know-is-her-name/> of whether we can predict someone=E2=80=99s age from th=
eir name. If you=E2=80=99re interested in the live stream idea, please leav=
e a comment on the page describing the project live_streams/2020-04-01-guessing-age-from-a-name> telling me when and how o=
ften you=E2=80=99d like to see something. All of these activities will be r=
ecorded and posted to YouTube for you to watch later if you can't join us. =
Please spread the word about these activities to your personal and virtual =
social networks.
As always, thank you for your support of mothur.
Take care of yourselves!
Pat
Enhancements:
Adds sra.info command to download and extract samples from NCBI using pref=
etch and fasterq-dump written by NCBI. #27 r/issues/27>
Adds make.clr command. #695
Adds clr file type to metastats command. #695 othur/issues/695>
Expands batch files. #601 #6=
58
Adds environment variables to mothur. #601 ur/issues/601>
Adds MOTHUR_TOOLS option to allow you to set the location of mothur's exte=
rnal tools at compile time or through the set.dir command at run time. #682=
Adds uchime parameter to chimera.uchime. #682 othur/issues/682>
Adds vsearch parameter to chimera.vsearch, cluster, cluster.split commands=
. #682
Improves mothur's checkorient option in make.contigs. Also sets checkorien=
t=3Dt by default.
split.abund command 's cutoff parameter can now be a percentage. Removes f=
asta file requirement. #263
Adds contigsreport to get.seqs and remove.seqs commands. #660 hub.com/mothur/mothur/issues/660>
Adds processors option to split.groups. #685 thur/issues/685>
Adds sets to remove.groups and get.groups commands. #277 om/mothur/mothur/issues/277>
Adds parallelization to chimera.vsearch when using denovo method. #700 tps://github.com/mothur/mothur/issues/700>
Changes filter.seqs fasta file delimantor from '-' to '|' to allow for '-'=
's in filenames.
Adds list file output for make.shared with count table.
Bugs:
Fixes tree.shared distance being used instead of similarity.
Fixes bug with remove.seqs not removing empty groups from the count table.=
#675
Fixes bug with trim.seqs if no name file is given and allfiles=3DT. #696 <=
https://github.com/mothur/mothur/issues/696>
Fixes corr.axes bug when metadata files contain zeroed columns.
-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-=3D-
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--Apple-Mail=_BEF47628-6B45-4443-A66F-D079A56B0801
Content-Transfer-Encoding: quoted-printable
Content-Type: text/html;
charset=utf-8
=
=3Dutf-8">space; line-break: after-white-space;" class=3D"">=3D"word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-whi= te-space;" class=3D""> bkit-nbsp-mode: space; line-break: after-white-space;" class=3D""> =3D"auto" style=3D"word-wrap: break-word; -webkit-nbsp-mode: space; line-b= reak: after-white-space;" class=3D""> break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class= = =3D""> rgb(36, 41, 46); font-size: 14px;" class=3D"">Hello mothur users,iv> color: rgb(36, 41, 46);" class=3D"">
: 14px;" class=3D"">We are happy to announce the release of pan>le=3D"font-size: 14px;" class=3D"">mothur v.1.44.0! 2e" class=3D"">an style=3D"font-size: 14px;" class=3D""> There are a number of other=
things to tell you about that coincide with this release.
span>
First, in t=
his release we have a number of new commands, feature enhancements, and bug=
fixes. To help foster reproducibility, we have created the pan>othur.org/wiki/sra.info/" class=3D"">sra.infoass=3D""> com=
mand, which will help you to download sequence data from the SRA and prepar=
e it for analysis with the typical mothur pipelines. We have also added the=
">make.clr command, which appli=
es the centered log-ratio transformation of OTU abundance data. This is a p=
opular approach to accounting for the compositional nature of microbiome se=
quence data. Although mothur=E2=80=99s r.org/wiki/pre.cluster/" class=3D"">pre.clusterclass=3D""> is arguably one of the first methods of assigning sequence=
s to amplicon/exact sequence variants, we never made it super easy to go fr=
om a count table file to a shared file. Although I still have some reservat=
ions about ASV/ESVs, with this release r.org/wiki/make.shared/" class=3D"">make.sharedclass=3D""> will take a count table and create a shared and list file =
for you. This is demonstrated in the org/wiki/miseq_sop/" class=3D"">MiSeq SOP=3D"">. Finally, for those of you that are fans of the =
=3D"https://mothur.org/wiki/batch_mode/" class=3D"">batch mode<= font color=3D"#24292e" class=3D""> ""> feature in mothur, we have added a number of new features to impro=
ve their utility including the ability to use your operating system=E2=80=
=99s environment variables.
e=3D"font-size: 14px; caret-color: rgb(36, 41, 46);" class=3D"">Second, Dec=
ember marked the 10th anniversary of the publishing of the nt> 4px;" class=3D"">paper describing mothur=3D"font-size: 14px;" class=3D"">6);" class=3D"">. This spring, AEM published a ref=3D"https://aem.asm.org/content/86/2/e02343-19" style=3D"font-size: 14px=
;" class=3D"">retrospective mini-review"">"> of mothur's development and the lesson's we've learned over the pas=
t 10 years. Even though it focuses on mothur, I think the lessons are =
generally valuable. We are grateful to all the past and current mothur user=
s that have helped to shape mothur.
nt style=3D"caret-color: rgb(36, 41, 46); font-size: 14px;" class=3D"">Thir=
d, if you've been to the " class=3D"">mothur website<=
/a>1, 46);" class=3D""> you'll noticed that it has received a major rewor=
k. We had been experiencing some hosting and general security problems=
over the years that recently escalated. It has been transformed to a Jekyl=
l-based wiki that is written in s.github.com/features/mastering-markdown/" class=3D"">markdownont color=3D"#24292e" class=3D"">"> hosted on GitHub. You=E2=80=99ll also notice that=
the formulae for the calculators now render correctly. Please let us know =
if you see a problem with any of the documentation by clicking on the =
GitHub link on the page. This would also be an excellent time to get your o=
wn GitHub account if you don't have one already!
=
e: 14px;" class=3D"">Fourth, like many of you, we are adjusting to a new wa=
y of trying to do science. There are more important things going on in the =
world right now than finding the best way to analyze sequence data. Th=
at being said, if you have the mental and time bandwidth, I would encourage=
you to check out our free resources for learning to program and make =
your data analyses more reproducible. Over the years, I've developed an&nbs=
p;://www.riffomonas.org/minimalR/" class=3D"">extensive R tutorialolor=3D"#24292e" class=3D"">lass=3D""> for analyzing mothur output and a series of lessons on=
rch/" class=3D"">reproducible research">. Starting Thurs=
day afternoon, I will be hosting an activity that has been successful in my=
lab called ub/" class=3D"">Code Club=
=3D"caret-color: rgb(36, 41, 46);" class=3D"">, which is an interacti=
ve way to help people develop and strengthen their programming skills. It i=
s designed to serve people of all skill levels and will involve working wit=
h data from diverse sources. Next week, I will start to =
live=
stream a data=
analysis project that I will run through YouTube. I welcome your participa=
tion during the stream. To keep things light during this time stressful tim=
e, I will re-analyze and expand upon fivethirtyeight.com/features/how-to-tell-someones-age-when-all-you-know-is-=
her-name/" class=3D"">Five Thirty Eight=E2=80=99s question=3D"#24292e" class=3D""> of whether we can predict s=
omeone=E2=80=99s age from their name. If you=E2=80=99re interested in the l=
ive stream idea, please leave a comment on the =3D"https://www.riffomonas.org/live_streams/2020-04-01-guessing-age-from-a=
-name" class=3D"">page describing the project92e" class=3D"">"> telling me when and how often you=E2=80=99d like to see something. =
All of these activities will be recorded and posted to YouTube for you=
to watch later if you can't join us. Please spread the word about these ac=
tivities to your personal and virtual social networks.
>
41, 46);" class=3D"">As always, thank you for your support of mothur.t>
: rgb(36, 41, 46);" class=3D"">Take care of yourselves!
">>Pat
nt>b(36, 41, 46); color: rgb(36, 41, 46); margin-top: 0px !important;" class=
=3D"">Enhancements: =
rgin-bottom: 16px; caret-color: rgb(36, 41, 46); color: rgb(36, 41, 46);" c=
lass=3D"">- ont-size: 14px;" class=3D"">Adds sra=
.info command to download and extract samples from NCBI using prefetch =
and fasterq-dump written by NCBI. " data-error-text=3D"Failed to load title" data-id=3D"54935575" data-permis=
sion-text=3D"Title is private" data-url=3D"https://github.com/mothur/mothur=
/issues/27" data-hovercard-type=3D"issue" data-hovercard-url=3D"/mothur/mot=
hur/issues/27/hovercard" href=3D"https://github.com/mothur/mothur/issues/27=
" style=3D"box-sizing: border-box; color: rgb(3, 102, 214); text-decoration=
: none;">#27 - : 0.25em;" class=3D"">Adds make=
.clr command. "Failed to load title" data-id=3D"550904296" data-permission-text=3D"Title =
is private" data-url=3D"https://github.com/mothur/mothur/issues/695" data-h=
overcard-type=3D"issue" data-hovercard-url=3D"/mothur/mothur/issues/695/hov=
ercard" href=3D"https://github.com/mothur/mothur/issues/695" style=3D"box-s=
izing: border-box; color: rgb(3, 102, 214); text-decoration: none;">#695> - s=3D"">Adds clr file type to me=
tastats command. =
=3D"Failed to load title" data-id=3D"550904296" data-permission-text=3D"Ti=
tle is private" data-url=3D"https://github.com/mothur/mothur/issues/695" da=
ta-hovercard-type=3D"issue" data-hovercard-url=3D"/mothur/mothur/issues/695=
/hovercard" href=3D"https://github.com/mothur/mothur/issues/695" style=3D"b=
ox-sizing: border-box; color: rgb(3, 102, 214); text-decoration: none;">#69=
5 - class=3D"">Expands batch files.=
ad title" data-id=3D"429824073" data-permission-text=3D"Title is private" d=
ata-url=3D"https://github.com/mothur/mothur/issues/601" data-hovercard-type=
=
=3D"issue" data-hovercard-url=3D"/mothur/mothur/issues/601/hovercard" href=
=
=3D"https://github.com/mothur/mothur/issues/601" style=3D"box-sizing: bord=
er-box; color: rgb(3, 102, 214); text-decoration: none;">#601 lass=3D"issue-link js-issue-link" data-error-text=3D"Failed to load title" =
data-id=3D"495784845" data-permission-text=3D"Title is private" data-url=3D=
"https://github.com/mothur/mothur/issues/658" data-hovercard-type=3D"issue"=
data-hovercard-url=3D"/mothur/mothur/issues/658/hovercard" href=3D"https:/=
/github.com/mothur/mothur/issues/658" style=3D"box-sizing: border-box; colo=
r: rgb(3, 102, 214); text-decoration: none;">#658 - =3D"box-sizing: border-box; margin-top: 0.25em;" class=3D"">"font-size: 14px;" class=3D"">Adds environment variables to mothur. class=3D"issue-link js-issue-link" data-error-text=3D"Failed to load title=
" data-id=3D"429824073" data-permission-text=3D"Title is private" data-url=
=3D"https://github.com/mothur/mothur/issues/601" data-hovercard-type=3D"is=
sue" data-hovercard-url=3D"/mothur/mothur/issues/601/hovercard" href=3D"htt=
ps://github.com/mothur/mothur/issues/601" style=3D"box-sizing: border-box; =
color: rgb(3, 102, 214); text-decoration: none;">#601 - yle=3D"box-sizing: border-box; margin-top: 0.25em;" class=3D"">=3D"font-size: 14px;" class=3D"">Adds MOTHUR_TOOLS option to allow you to =
set the location of mothur's external tools at compile time or through the =
set.dir command at run time. a-error-text=3D"Failed to load title" data-id=3D"516141179" data-permission=
-text=3D"Title is private" data-url=3D"https://github.com/mothur/mothur/iss=
ues/682" data-hovercard-type=3D"issue" data-hovercard-url=3D"/mothur/mothur=
/issues/682/hovercard" href=3D"https://github.com/mothur/mothur/issues/682"=
style=3D"box-sizing: border-box; color: rgb(3, 102, 214); text-decoration:=
none;">#682 - : 0.25em;" class=3D"">Adds uchi=
me parameter to chimera.uchime. data-error-text=3D"Failed to load title" data-id=3D"516141179" data-permiss=
ion-text=3D"Title is private" data-url=3D"https://github.com/mothur/mothur/=
issues/682" data-hovercard-type=3D"issue" data-hovercard-url=3D"/mothur/mot=
hur/issues/682/hovercard" href=3D"https://github.com/mothur/mothur/issues/6=
82" style=3D"box-sizing: border-box; color: rgb(3, 102, 214); text-decorati=
on: none;">#682 - top: 0.25em;" class=3D"">Adds v=
search parameter to chimera.vsearch, cluster, cluster.split commands. =
le" data-id=3D"516141179" data-permission-text=3D"Title is private" data-ur=
l=3D"https://github.com/mothur/mothur/issues/682" data-hovercard-type=3D"is=
sue" data-hovercard-url=3D"/mothur/mothur/issues/682/hovercard" href=3D"htt=
ps://github.com/mothur/mothur/issues/682" style=3D"box-sizing: border-box; =
color: rgb(3, 102, 214); text-decoration: none;">#682 - yle=3D"box-sizing: border-box; margin-top: 0.25em;" class=3D"">=3D"font-size: 14px;" class=3D"">Improves mothur's checkorient option in m=
ake.contigs. Also sets checkorient=3Dt by default. - box-sizing: border-box; margin-top: 0.25em;" class=3D"">-size: 14px;" class=3D"">split.abund command 's cutoff parameter can now be=
a percentage. Removes fasta file requirement. js-issue-link" data-error-text=3D"Failed to load title" data-id=3D"17013367=
6" data-permission-text=3D"Title is private" data-url=3D"https://github.com=
/mothur/mothur/issues/263" data-hovercard-type=3D"issue" data-hovercard-url=
=
=3D"/mothur/mothur/issues/263/hovercard" href=3D"https://github.com/mothur=
/mothur/issues/263" style=3D"box-sizing: border-box; color: rgb(3, 102, 214=
); text-decoration: none;">#263 - der-box; margin-top: 0.25em;" class=3D"">lass=3D"">Adds contigsreport to get.seqs and remove.seqs commands. class=3D"issue-link js-issue-link" data-error-text=3D"Failed to load title"=
data-id=3D"495958028" data-permission-text=3D"Title is private" data-url=
=3D"https://github.com/mothur/mothur/issues/660" data-hovercard-type=3D"is=
sue" data-hovercard-url=3D"/mothur/mothur/issues/660/hovercard" href=3D"htt=
ps://github.com/mothur/mothur/issues/660" style=3D"box-sizing: border-box; =
color: rgb(3, 102, 214); text-decoration: none;">#660 - yle=3D"box-sizing: border-box; margin-top: 0.25em;" class=3D"">=3D"font-size: 14px;" class=3D"">Adds processors option to split.groups.&n=
bsp; title" data-id=3D"519290805" data-permission-text=3D"Title is private" dat=
a-url=3D"https://github.com/mothur/mothur/issues/685" data-hovercard-type=
=3D"issue" data-hovercard-url=3D"/mothur/mothur/issues/685/hovercard" href=
=
=3D"https://github.com/mothur/mothur/issues/685" style=3D"box-sizing: bord=
er-box; color: rgb(3, 102, 214); text-decoration: none;">#685i> - n style=3D"font-size: 14px;" class=3D"">Adds sets to remove.groups and get.=
groups commands. =
=3D"Failed to load title" data-id=3D"180643897" data-permission-text=3D"Ti=
tle is private" data-url=3D"https://github.com/mothur/mothur/issues/277" da=
ta-hovercard-type=3D"issue" data-hovercard-url=3D"/mothur/mothur/issues/277=
/hovercard" href=3D"https://github.com/mothur/mothur/issues/277" style=3D"b=
ox-sizing: border-box; color: rgb(3, 102, 214); text-decoration: none;">#27=
7 - class=3D"">Adds parallelization=
to chimera.vsearch when using denovo method. s-issue-link" data-error-text=3D"Failed to load title" data-id=3D"564140410=
" data-permission-text=3D"Title is private" data-url=3D"https://github.com/=
mothur/mothur/issues/700" data-hovercard-type=3D"issue" data-hovercard-url=
=3D"/mothur/mothur/issues/700/hovercard" href=3D"https://github.com/mothur=
/mothur/issues/700" style=3D"box-sizing: border-box; color: rgb(3, 102, 214=
); text-decoration: none;">#700 - der-box; margin-top: 0.25em;" class=3D"">lass=3D"">Changes filter.seqs fasta file delimantor from '-' to '|' to allo=
w for '-''s in filenames. - argin-top: 0.25em;" class=3D"">=
Adds list file output for make.shared with count table. style=3D"box-sizing: border-box; margin-top: 0px; margin-bottom: 16px; care=
t-color: rgb(36, 41, 46); color: rgb(36, 41, 46);" class=3D"">=3D"font-size: 14px;" class=3D"">Bugs: > _._,_._,_
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