#Samtools

2025-02-16

@kaasbaas #wikipedia (English language) is only ~22GB of #bzip2 compressed #xml (uncompressed size is ~86GB).
is it possible to access it without decompression? I guess #random #access to .xml.bz2 should be a solved problem, right?
we're routinely using gzip with random access in #bioinformatics ie via #samtools or #tabix

EDIT:
Wikipedia xml.bz2 does support random access for multistream version. does @kiwix or any other wiki reader support it? I couldn't find info on their website...

2024-11-23

Just out: @multiqc v1.25.2 πŸŽ‰

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

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/MultiQC/rel

Pierre Lindenbaumyokofakun@genomic.social
2024-09-12

gcc -g -Wall -O2 -fvisibility=hidden -I. -c -o simd.o simd.c

simd.c:126:5: warning: implicit declaration of function β€˜_mm_lddqu_si128’ [-Wimplicit-function-declaration]
__m128i nuc_lookup_vec = _mm_lddqu_si128((__m128i *)seq_nt16_str);
^
simd.c:126:30: error: incompatible types when initializing type β€˜__m128i’ using type β€˜int’
__m128i nuc_lookup_vec = _mm_lddqu_si128((__m128i *)seq_nt16_str);

πŸ€” #samtools 1.21

2024-04-11

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, such as read unmapped and mate unmapped.
#genomics #bioinformatics
broadinstitute.github.io/picar

Pierre Lindenbaumyokofakun@genomic.social
2023-09-08

The PR for samtools (visualize CNVs in the #terminal ) was merged today ! #samtools #cnv #sv #structuralvariant #ascii github.com/samtools/samtools/p

Pierre Lindenbaumyokofakun@genomic.social
2023-08-30

I just wrote a new PR for `samtools coverage` to plot the depth instead of the '% of covered bases' . Useful to validate #CNV in the terminal. #samtools #bioinformatics #sv #variant #bam

github.com/samtools/samtools/p

2023-06-06

Split a #BAM file produced by #CellRanger into one file per #singlecell barcode, using #samtools and #awk:

samtools view in.bam | awk '/CB:Z:/{f=substr($0,match($0,/CB:Z:[ACGT]{16}/)+5,16)".txt"}{print>>f}'

Pierre Lindenbaumyokofakun@genomic.social
2023-01-22

asked #biostars "htslib/c what is the correct way to use bgzf_thread_pool ?" #C #samtools #htskib #fastq biostars.org/p/9551841/

Pierre Lindenbaumyokofakun@genomic.social
2022-12-01

plot depth of #coverage in the #terminal using #samtools #depth and gnuplot:

```
$ samtools depth -a -r "chr1:234-456" in.bam | cut -f 2,3 | gnuplot -e 'set terminal dumb size 120,28; plot "-" smooth csplines with lines notitle'
```

#linux #bioinformatics

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