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Samtools Team (@htslib) profile picture

Samtools Team

@htslib

Announcements of samtools, bcftools, and htslib releases. See the website for documentation, pointers to support and mailing lists, etc.

htslib.org
Joined July 2014
  • Tweets77
  • Following12
  • Followers1.1K
Samtools Team retweeted
Petr Danecek (@petrdanecek) profile picture
Petr Danecek@petrdanecek17 Feb 2021
Play it again, SAM(tools)? gigasciencejournal.com/blog/…
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Samtools Team retweeted
Petr Danecek (@petrdanecek) profile picture
Petr Danecek@petrdanecek17 Feb 2021
HTSlib paper academic.oup.com/gigascience…
HTSlib: C library for reading/writing high-throughput sequencing data

HTSlib: C library for reading/writing high-throughput sequencing data

AbstractBackground. Since the original publication of the VCF and SAM formats, an explosion of software tools have been created to process these data files

academic.oup.com
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Samtools Team retweeted
Petr Danecek (@petrdanecek) profile picture
Petr Danecek@petrdanecek17 Feb 2021
Twelve years of SAMtools and BCFtools academic.oup.com/gigascience…
Twelve years of SAMtools and BCFtools

Twelve years of SAMtools and BCFtools

AbstractBackground. SAMtools and BCFtools are widely used programs for processing and analysing high-throughput sequencing data. They include tools for fil

academic.oup.com
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Samtools Team retweeted
John Marshall (@jomarnz) profile picture
John Marshall@jomarnz6 Oct 2016
Replying to @htslib
We'd like to hear if anyone is using this undocumented @htslib facility. Pls comment on issue. Suspect they're unused outside our testsuite.
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Samtools Team retweeted
Erik Garrison (@erikgarrison) profile picture
Erik Garrison@erikgarrison3 Oct 2016
freebayes is now 4x faster and many times lighter in RAM thanks to @JeremiahWala's integration of SeqLib github.com/ekg/freebayes/pul… !!!

SeqLib integration (HTSlib-based BamTools switch) by walaj · Pull Request #316 · freebayes/freebayes

Hi Erik, I have been working on an HTSlib based C++ API, as I was finding that with as much BAM access as I was doing, that switching to HTSlib was able to really speed things up over BamTools. I r...

github.com
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Samtools Team retweeted
John Marshall (@jomarnz) profile picture
John Marshall@jomarnz21 Sep 2016
Posters on @htslib at #gi2016 tonight: new HTSlib faciliities (poster 60), and good news for Perl users (Bio-DB-HTS, poster 64)
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Samtools Team retweeted
Aaron Quinlan (@aaronquinlan) profile picture
Aaron Quinlan@aaronquinlan6 Jul 2016
Just dropped #bedtools v2.26. Many bug fixes and new features. Strongly rec. an update! Next focus is CRAM support. github.com/arq5x/bedtools2/r…
Release bedtools version 2.26.0 · arq5x/bedtools2

Release bedtools version 2.26.0 · arq5x/bedtools2

Fixed a major memory leak when using -sorted. Thanks to Emily Tsang and Stephen Montgomery. Fixed a bug for BED files containing a single record with no newline. Thanks to @jmarshall. The getfasta ...

github.com
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Samtools Team retweeted
John Marshall (@jomarnz) profile picture
John Marshall@jomarnz22 Apr 2016
Replying to @htslib
Bugs squashed include better error checking in @htslib & samtools, and race conditions involving ref cache files & sort temp files resolved
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Samtools Team retweeted
Heng Li (@lh3lh3) profile picture
Heng Li@lh3lh324 Feb 2016
bwa-0.1.13 released; mostly a bug fix release: github.com/lh3/bwa/releases Also, an Apache2 version of bwa at: github.com/lh3/bwa/tree/Apac…

Releases · lh3/bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment) - lh3/bwa

github.com
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freebayes turns v1.0.0 with initial support for gVCF github.com/ekg/freebayes/rel…
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Samtools Team retweeted
Adam Auton (@adamauton) profile picture
Adam Auton@adamauton27 Oct 2015
Replying to @gatk_dev
@gatk_dev @pathogenomenick but still available as standalone as well?
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Samtools Team retweeted
Devon Ryan (@dpryan79) profile picture
Devon Ryan@dpryan7922 Sep 2015
[github] Added dpryan79/libBigWig: A C library for handling bigWig files ift.tt/1ONOOAC
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Samtools Team retweeted
Devon Ryan (@dpryan79) profile picture
Devon Ryan@dpryan792 Jun 2015
Some impressive CRAMv3 benchmarks from jkb @htslib: htslib.org/benchmarks/CRAM.h…
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Samtools Team retweeted
Ewan Birney (@ewanbirney) profile picture
Ewan Birney@ewanbirney4 Mar 2015
Samtools developers, as part of @GA4GH getting their beer for CRAM integration in production - come on @gatk_dev :)
Image from Ewan Birney (@ewanbirney)
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Samtools Team retweeted
Wolfgang Resch (@WolfResch) profile picture
Wolfgang Resch@WolfResch18 Nov 2014
Replying to @htslib
@htslib I wrote a short post on processing a VCF file with htslib: wresch.github.io/2014/11/18/…. Maybe useful since there aren't many docs yet.
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