#samtools

Matej Lexa

@matej-lexa.scicomm.xyz.ap.brid.gy

5 months ago

My PhD student authored a rather niche piece of software written in Rust that introduces a new type of index for BAM files, allowing fast counting and filtering of reads based on their FLAG attributes […]

Ken Koon Wong

@kenkoonwong.bsky.social

5 months ago

Exploring The Workflow of The Oxford Nanopore Technologies (ONT) from pod5 to Polished Asembly - A Note To Myself | Everyday Is A School Day Hands-on with Oxford Nanopore workflow: pod5 → BAM → assembly! Processed M. tuberculosis from raw signals to complete genome using dorado + flye. Fascinating how thousands of contigs became one 4M+ bp...

Hands-on with @nanoporetech.com workflow: pod5 → BAM → assembly -> polish! Processed M. tuberculosis from raw signals to complete genome using #dorado + #samtools + #flye. Fascinating how thousands of contigs became one 4M+ bp sequence.

#idsky #tbsky #microsky #bioinformatics

SMT

@pp0196.bsky.social

7 months ago

#kmers #Bioinformatics #Ancestry #lowpass
Dependencies: #RStats #Perl #samtools #GenomeTester4

Andrew Whitwham

@whitwham.bsky.social

9 months ago

Release 1.22 of HTSlib, SAMtools, and BCFtools is now available from GitHub. See htslib.org/download/ for links to tarballs and release notes. 🧪

#samtools #bcftools #htslib #bioinformatics

Hywel Williams

@genefiddler.bsky.social

1 year ago

OK #bioinformatics folk, I am in dire need of help as after 3 weeks of trying I'm stumped.

I have a bam file that was aligned to GRCh38 with alt contigs but I need to remove the alt contigs fromthe file and header.

I've used #samtools and #Picard

1/2

Heinrich Ferreira

@heinrichferreira.bsky.social

1 year ago

How to build SAMTOOLS on a Windows PC How to compile SAMTOOLS.exe as a 64 bit executable for windows PCs.

Here are step by step instructions I recently made on how to build a 64 bit Windows exe of SAMTOOLS on a Windows PC.
I am currently busy integrating it into the Visual Genome Browser.
#bioinformatics
#bioinformaticstools
#samtools
#genomics

splicejunction.blogspot.com/2025/01/how-...

MultiQC

@multiqc.info

1 year ago

Release v1.25.2 · MultiQC/MultiQC MultiQC v1.25.2 - 2024-11-20 Multiple bug fixes and minor updates. Updates Add natural sort for sample sorting (#2959) Custom content: for plot_type: image, support custom_data config with section...

Just out: @multiqc.info v1.25.2 🎉

This patch release fixes a whole host of bugs, the most important one being for #bcl2fastq 🐛

There are also a host of small additions sneaking in for #ngsbits, #picard, #Nanostat, #Samtools and more - so well worth the update!

github.com/MultiQC/Mult...

Luke Pembleton

@lwpembleton.bsky.social

1 year ago

I was reminded of this helpful tool the other day to identify SAM/BAM/CRAM flag values. Great when you are hacking away with #samtools view commands and need to know the flag number to filter based on read properties. #genomics #Bioinformatics
Explain SAM Flags (broadinstitute.github.io)

Martin Smith

@martinalexsmith.bsky.social

9 years ago

I just created a bash alias bamtools="samtools" because I have 2 young kids and don't get much sleep #bioinformatics #genomics #samtools