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

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)

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

Analysis pipeline for processing paired-end Illumina reads obtained after ancient mtDNA target enrichment capture.

Installation and usage for various tools for cancer genomics

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

Snakemake pipeline for Popoolation and Popoolation2

Collecting Genotypes from ENA and make their SNPs