9 results found Sort:

mdshw5
pyfaidx mdshw5
75
463
other
9
Efficient pythonic random access to fasta subsequences
dna bgzf fasta python protein genomics indexing samtools bioinformatics
Created 2013-09-12
879 commits to master branch, last one 2 months ago
seqan
seqan3 seqan
82
414
other
25
The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.
blast cpp20 fasta fastq seqan modern fm-index samtools cpp-concepts bioinformatics sequence-analysis sequence-alignment
Created 2016-04-04
6,845 commits to main branch, last one a day ago
biowasm
biowasm biowasm
23
227
mit
10
WebAssembly modules for genomics
jq awk sed grep seqtk bowtie2 bedtools genomics minimap2 samtools javascript webassembly bioinformatics
Created 2019-09-07
1,193 commits to main branch, last one 17 days ago
wheretrue
biobear wheretrue
11
165
mit
3
Work with bioinformatic files using Arrow, Polars, and/or DuckDB
arrow duckdb polars python biology pyarrow rust-bio samtools biopython bioinformatics
Created 2023-04-22
299 commits to main branch, last one 6 days ago
divonlan
genozip divonlan
12
161
other
1
A modern compressor for genomic files (FASTQ, SAM/BAM/CRAM, VCF, FASTA, GFF/GTF/GVF, 23andMe...), up to 5x better than gzip and faster too
bam bwa gvf sam vcf cram gzip bgzip fasta fastq 23andme genomics samtools compression
Created 2019-12-15
3,265 commits to master branch, last one 15 days ago
ngless-toolkit
ngless ngless-toolkit
25
144
other
11
NGLess: NGS with less work
bwa ngs fastq haskell science genomics samtools fastq-format metagenomics bioinformatics haskell-language bioinformatics-pipeline next-generation-sequencing
Created 2013-01-08
2,453 commits to main branch, last one 4 months ago
davetang
learning_bam_file davetang
22
110
mit
8
Learning the Sequence Alignment/Map format
bam sam samtools bam-files bam-flags
Created 2016-04-15
94 commits to main branch, last one 9 months ago
IARCbioinfo
needlestack IARCbioinfo
15
50
gpl-3.0
11
Multi-sample somatic variant caller
ngs docker nextflow pipeline samtools variants bam-files regression somatic-mutations negative-binomial-regression
Created 2015-06-16
981 commits to master branch, last one 5 years ago
digo4
Clinical-Genomics digo4
11
40
mit
3
Here we are going to discuss variant calling on human datasets using GATK Best practices pipeline
fastp gatk4 fastqc picard bowtie2 bwa-mem varscan bcftools cutadapt gatk-cnv samtools freebayes trimgalore trimmomatic gatk-bestpractices gatk4-haplotypecaller gatk-joint-variant-calling-workflow
Created 2023-12-22
69 commits to main branch, last one 11 months ago