There are 2 repositories under samtools topic.
The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.
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: NGS with less work
Learning the Sequence Alignment/Map format
Multi-sample somatic variant caller
Here we are going to discuss variant calling on human datasets using GATK Best practices pipeline
Genopo a.k.a. F5N - A nanopore sequencing analysis toolkit for Android smartphones https://nanoporetech.com
A command line tool (in Kotlin/JVM) for intuitively visualizing BAM alignments. (Currently unmaintained)
RNAseq pipeline for alternative splicing junctions
Analysis pipeline for processing paired-end Illumina reads obtained after ancient mtDNA target enrichment capture.
Snakemake pipeline for Popoolation and Popoolation2
Installation and usage for various tools for cancer genomics
Library-free horizontal transfer detection, with a focus on transposable element invasions
Collecting Genotypes from ENA and make their SNPs
Get sex info from BAM file
For comparing the subgenomes of wheat
VariantCaller is a wrapper for the 2022 gatk & bcftools best practices + phasing with WhatsHap.
Fast, epiallele-aware methylation caller and reporter — an R/Bioconductor package
Command line utility written in NodeJS to decode SAM flags to explain what they mean.
Take information about snps on short sequence reads and accurately place the snps in a reference genome
Some NGS library preps use amplicons, and it can be difficult to determine the coverage and depth of each amplicon.
A simple Nextflow pipeline for testing the performance of sambamba vs samtools
Repository for course project in Bioinformatics Institute 2023-2024
Tools to filter SAM/BAM files by percent identity and percent of matched sequence
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).