There are 2 repositories under samtools topic.
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
RNAseq pipeline for alternative splicing junctions
A command line tool (in Kotlin/JVM) for intuitively visualizing BAM alignments. (Currently unmaintained)
Analysis pipeline for processing paired-end Illumina reads obtained after ancient mtDNA target enrichment capture.
Collecting Genotypes from ENA and make their SNPs
🛠 under active development | RNA-Seq Workflow in Jupyter Notebook
Installation and usage for various tools for cancer genomics
For comparing the subgenomes of wheat
Snakemake pipeline for Popoolation and Popoolation2
Library-free horizontal transfer detection, with a focus on transposable element invasions
Get sex info from BAM file
Fast, epiallele-aware methylation caller and reporter — an R/Bioconductor package
A simple Nextflow pipeline for testing the performance of sambamba vs samtools
Apply samtools addreplacerg to add a new read group and assign all reads to it in a BAM file
VariantCaller is a wrapper for the 2022 gatk & bcftools best practices + phasing with WhatsHap.