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DATE 2022-08-01

LEARN

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Key: Value:

Key: Value:

MESSAGE

DATE	2022-08-31
FROM	From: "Pat Schloss"
SUBJECT	Subject: [Learn] [mothur] mothur v1.48.0 release / MiSeq SOP update /
From learn-bounces-at-nylxs.com Thu Sep 1 13:37:01 2022 Return-Path: X-Original-To: archive-at-mrbrklyn.com Delivered-To: archive-at-mrbrklyn.com Received: from www2.mrbrklyn.com (www2.mrbrklyn.com [96.57.23.82]) by mrbrklyn.com (Postfix) with ESMTP id 3349F164059; Thu, 1 Sep 2022 13:37:01 -0400 (EDT) X-Original-To: learn-at-www2.mrbrklyn.com Delivered-To: learn-at-www2.mrbrklyn.com Received: by mrbrklyn.com (Postfix, from userid 1000) id F0048164056; Thu, 1 Sep 2022 13:36:58 -0400 (EDT) Resent-From: Ruben Safir Resent-Date: Thu, 1 Sep 2022 13:36:58 -0400 Resent-Message-ID: <20220901173658.GA3383-at-www2.mrbrklyn.com> Resent-To: learn-at-mrbrklyn.com X-Original-To: ruben-at-mrbrklyn.com Delivered-To: ruben-at-mrbrklyn.com Received: from web01.groups.io (web01.groups.io [66.175.222.12]) (using TLSv1.2 with cipher ECDHE-RSA-AES128-GCM-SHA256 (128/128 bits)) (Client did not present a certificate) by mrbrklyn.com (Postfix) with ESMTPS id D0F3016403D for ; Wed, 31 Aug 2022 15:43:53 -0400 (EDT) X-Received: by 127.0.0.2 with SMTP id AeQnYY322857xdd1XWLHrO6; Wed, 31 Aug 2022 12:43:52 -0700 X-Received: from mail-qv1-f42.google.com (mail-qv1-f42.google.com [209.85.219.42]) by mx.groups.io with SMTP id smtpd.web12.3380.1661975029520755764 for ; Wed, 31 Aug 2022 12:43:50 -0700 X-Received: by mail-qv1-f42.google.com with SMTP id d1so11917935qvs.0 for ; Wed, 31 Aug 2022 12:43:49 -0700 (PDT) X-Gm-Message-State: xbjHAKC1cebmfN4Rm2RHw7Nux321522AA= X-Google-Smtp-Source: AA6agR4Ud0BbJGMa4RKZI9/D3UH6+sqCk9N3kM6UcI/Ld4BDGs+Iq3T2uMEGNrRBkuRwz8pU4Gl+OZPQHAURD8YnYJc= X-Received: by 2002:a05:6214:2aa2:b0:477:1882:3dc with SMTP id js2-20020a0562142aa200b00477188203dcmr20823339qvb.11.1661975028229; Wed, 31 Aug 2022 12:43:48 -0700 (PDT) MIME-Version: 1.0 From: "Pat Schloss" Date: Wed, 31 Aug 2022 15:43:37 -0400 Message-ID: To: mothur-at-groups.io Precedence: Bulk Mailing-List: list mothur-at-groups.io; contact mothur+owner-at-groups.io Delivered-To: mailing list mothur-at-groups.io DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/simple; d=groups.io; q=dns/txt; s=20140610; t=1661975032; bh=tneP/DvUDsY0ksGUoPRuECPOq8Y8DAEF8GKkMvTNCcI=; h=Content-Type:Date:From:Reply-To:Subject:To; b=Mi9y7fSld9MSz/7+mAvVHMqEzCuEs3IysyZu+ea+7h2nbhmoRk/3BVpQHspfombUNNh 1JxrkNBwbTe87NTdb1kVpfwrswnnCvqGapKoGjD8EVTA2c934gGrlz66yujqiWP1q/Hr1 8mMDfPl1D38yxCajpM9sW79bIyaH1/qNkiQ= Subject: [Learn] [mothur] mothur v1.48.0 release / MiSeq SOP update / workshop X-BeenThere: learn-at-nylxs.com X-Mailman-Version: 2.1.30rc1 List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Reply-To: mothur-at-groups.io Content-Type: multipart/mixed; boundary="===============1586511576==" Errors-To: learn-bounces-at-nylxs.com Sender: "Learn" --===============1586511576== Content-Type: multipart/alternative; boundary="0000000000002f1c2f05e78eb7a8" --0000000000002f1c2f05e78eb7a8 Content-Type: text/plain; charset="UTF-8" Hello mothur users! We are happy to announce the release of mothur v.1.48.0 . Actually... we released 1.48 in May, but I never got around to telling anyone :) There are a few significant things to report with this release. The main improvements include improving the execution speed on a few functions and completing the transition of a few functions to output/input count files over group files. There's a few other things you might be interested in. Go ahead and check them out over at the release page when you get your new version of mothur ;) With the last version we started to shudder the use of a names and group file throughout the mothur workflow. We showed both the old and new workflows in the MiSeq SOP wiki page. While I think this helped people transition, it also caused some confusion for folks. This week, I went in and removed vestiges of the old workflow. Be sure to go check out the MiSeq SOP page if you have questions about how we recommend processing 16S rRNA gene sequences with mothur. This is the workflow that we use in the lab! Finally, I continue to put a lot of effort into developing educational content that should be of interest to mothur users. I am posting two videos each week to YouTube that often uses mothur-based files as input to work within R. You can find these at the Riffomonas YouTube channel . Earlier this year I talked a fair amount about the problems with not rarefying your data in these videos. Hopefully, I'll get a preprint up on biorxiv in the next month or so. If you are interested in the mothur workshop I'll be running at the end of September, be sure to check out the schedule . If you're looking for more updates on Riffomonas and resources for strengthening your R skills, I have a free weekly newsletter that you can subscribe to. I've been encouraged by the positive feedback I've received from the content on Riffomonas - let me know if there's anything you'd like me to be sure to cover. Enjoy the new release! Pat -=-=-=-=-=-=-=-=-=-=-=- Groups.io Links: You receive all messages sent to this group. View/Reply Online (#37): https://groups.io/g/mothur/message/37 Mute This Topic: https://groups.io/mt/93379509/321522 Group Owner: mothur+owner-at-groups.io Unsubscribe: https://groups.io/g/mothur/leave/10134514/321522/2086763283/xyzzy [ruben-at-mrbrklyn.com] -=-=-=-=-=-=-=-=-=-=-=- --0000000000002f1c2f05e78eb7a8 Content-Type: text/html; charset="UTF-8" Content-Transfer-Encoding: quoted-printable Hello=C2=A0mothur=C2=A0u= sers! We are happy to announce the release of=C2=A0mothur=C2=A0ef=3D"https://github.com/mothur/mothur/releases/tag/v1.48.0" target=3D"_bla= nk">v.1.48.0. Actually...=C2=A0 we released 1.48 in May, but I never go= t around to telling anyone :) There are a few significant things to report = with this release. The main improvements=C2=A0include improving the executi= on speed on a few functions and completing the transition of a few function= s to output/input count files over group files. There's a few other thi= ngs you might be interested in. Go ahead and check them out over at the=C2= =A0t=3D"_blank">release page=C2=A0when you get your new version of mothur = ;) With the last version we started to= shudder the use of a names and group file throughout the mothur workflow. = We showed both the old and new workflows in the MiSeq SOP wiki page. While = I think this helped people=C2=A0transition, it also caused some confusion f= or folks. This week, I went in and removed=C2=A0vestiges of the old workflo= w. Be sure to go check out the /">MiSeq SOP page if you have questions about how we recommend processi= ng 16S rRNA gene sequences with mothur. This is the workflow that we use in= the lab! Finally, I conti= nue to put a lot of effort into developing educational content that should = be of interest to mothur users. I am posting two videos each week to YouTub= e that often uses mothur-based files as input to work within R. You can fin= d these at the=C2=A0 target=3D"_blank">Riffomonas YouTube channel. Earlier this year I talk= ed a fair amount about the problems with not rarefying your data in these= videos. Hopefully, I'll get a preprint up on biorxiv in the next month= or so. If you are interested in the mothur workshop I'll be running at= the end of September, be sure to check out the as.org/workshops/2022-09-28-mothur.html">schedule.=C2=A0If you're l= ooking for more updates on Riffomonas and resources for strengthening your = R skills, I have a=C2=A0t=3D"_blank">free weekly newsletter=C2=A0that you can subscribe to. I&#= 39;ve been encouraged by the positive feedback I've received from the c= ontent on Riffomonas - let me know if there's anything you'd like m= e to be sure to cover. Enjoy the new release! = Pat _._,_._,_ G= roups.io Links: You receive all messages sent to this group. target=3D"_blank" href=3D"https://groups.io/g/mothur/message/37">View/Repl= y Online (#37) \| subject=3DRe:%20%5Bmothur%5D%20mothur%20v1.48.0%20release%20%2F%20MiSeq%20S= OP%20update%20%2F%20workshop">Reply To Group \| ef=3D"mailto:pschloss-at-umich.edu?subject=3DPrivate:%20Re:%20%5Bmothur%5D%20m= othur%20v1.48.0%20release%20%2F%20MiSeq%20SOP%20update%20%2F%20workshop">Re= ply To Sender \| 379509/321522">Mute This Topic \| /post">New Topic 21522">Your Subscription \| Co= ntact Group Owner \| 14/321522/2086763283/xyzzy">Unsubscribe [ruben-at-mrbrklyn.com] width=3D"1" style=3D"color:white;clear:both">_._,_._,_ =20 --0000000000002f1c2f05e78eb7a8-- --===============1586511576== Content-Type: text/plain; charset="us-ascii" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Content-Disposition: inline _______________________________________________ Learn mailing list Learn-at-nylxs.com http://lists.mrbrklyn.com/mailman/listinfo/learn --===============1586511576==--