samtools
There are 89 repositories under samtools topic.
mdshw5/pyfaidx
Efficient pythonic random access to fasta subsequences
seqan/seqan3
The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.
biowasm/biowasm
WebAssembly modules for genomics
divonlan/genozip
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
ngless-toolkit/ngless
NGLess: NGS with less work
wheretrue/biobear
Work with bioinformatic files using Arrow, Polars, and/or DuckDB
davetang/learning_bam_file
Learning the Sequence Alignment/Map format
IARCbioinfo/needlestack
Multi-sample somatic variant caller
nf-core/hgtseq
A pipeline to investigate horizontal gene transfer from NGS data
digo4/Clinical-Genomics
Here we are going to discuss variant calling on human datasets using GATK Best practices pipeline
odb9402/CNNPeaks
The ChIP-Seq peak calling algorithm using convolution neural networks
SanojPunchihewa/f5n
Genopo a.k.a. F5N - A nanopore sequencing analysis toolkit for Android smartphones https://nanoporetech.com
jslfree080/bamscope
A command line tool (in Kotlin/JVM) for intuitively visualizing BAM alignments. (Currently unmaintained)
LBGC-CFB/SpliceLauncher
RNAseq pipeline for alternative splicing junctions
mnievesc/Ancient_mtDNA_Pipeline
Analysis pipeline for processing paired-end Illumina reads obtained after ancient mtDNA target enrichment capture.
jlanga/smsk_popoolation
Snakemake pipeline for Popoolation and Popoolation2
qingxiangguo/Tools-for-Cancer-Genome-Analysis
Installation and usage for various tools for cancer genomics
rpianezza/GenomeDelta
Library-free horizontal transfer detection, with a focus on transposable element invasions
AmirHoseinSafari/Genotype-collector-and-SNP-dataset-creator
Collecting Genotypes from ENA and make their SNPs
adrianodemarino/Determine_sex_from_bam
Get sex info from BAM file
fachrulm/GenomeComparer
For comparing the subgenomes of wheat
irods-contrib/metalnx-msi
Metalnx Micro Services for iRODS
RhettRautsaw/VariantCaller
VariantCaller is a wrapper for the 2022 gatk & bcftools best practices + phasing with WhatsHap.
BBCG/epialleleR
Fast, epiallele-aware methylation caller and reporter — an R/Bioconductor package
cbp44/samflags
Command line utility written in NodeJS to decode SAM flags to explain what they mean.
CNuge/snp-placer
Take information about snps on short sequence reads and accurately place the snps in a reference genome
guigolab/sambamBench-nf
A simple Nextflow pipeline for testing the performance of sambamba vs samtools
IARCbioinfo/addreplacerg-nf
Apply samtools addreplacerg to add a new read group and assign all reads to it in a BAM file
iliapopov17/The-shadow-of-HIV
Repository for course project in Bioinformatics Institute 2023-2024
ionCRAM/ionCRAM
https://ioncram.saudigenomeproject.com/
kpatel427/bash
useful bash one-liners and scripts
r3fang/CRESTseq
CREST-seq peak calling.
Robaina/filterSAM
Tools to filter SAM/BAM files by percent identity and percent of matched sequence
TC-Hewitt/MuTrigo
Pipeline for gene candidate discovery based on mutagenesis. Featured in gene cloning research published in Nature (DOIs: 10.1038/s41467-020-14937-2, 10.1038/s41467-021-23738-0, 10.1038/s41477-021-00971-5), Molecular Plant (DOI: 10.1016/j.molp.2021.05.010) and New Phytologist (DOI: 10.1111/nph.17075).
y9c/cpup
Convert mpileup format to base count tsv table