samtools

Efficient pythonic random access to fasta subsequences

The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

WebAssembly modules for genomics

Work with bioinformatic files using Arrow, Polars, and/or DuckDB

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

A pipeline to investigate horizontal gene transfer from NGS data

Detecting transposable element invasions without repeat library. Detects also horizontal transfer events and endogenized viruses. All you need is a reference genome and some short reads

The ChIP-Seq peak calling algorithm using convolution neural networks

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.

Installation and usage for various tools for cancer genomics

Genopo a.k.a. F5N - A nanopore sequencing analysis toolkit for Android smartphones https://nanoporetech.com

Fast SAM/BAM sorter.

Snakemake pipeline for Popoolation and Popoolation2