C library for high-throughput sequencing data formats

A Java API for high-throughput sequencing data (HTS) formats.

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

VerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.

A DNA Sequence Alignment/Map (SAM) library for Clojure

Frequently used commands in bioinformatics

cram is a computational room acoustics module to simulate and explore various acoustic properties of a modeled space

ILIAD: A suite of automated Snakemake workflows for processing genomic data for downstream applications

Fast and accurate sequence demultiplexing

Functional tests for command line applications

A bioinformatics best-practice analysis pipeline for calling structural variants (SVs), copy number variants (CNVs) and repeat region expansions (RREs) from short DNA reads

A nextflow pipeline for calling and annotating small germline variants from short DNA reads for WES and WGS data

basepair bio: a single binary with many useful genomics subtools.

an API for intersections of genomic data

Rust software for solving impartial games.

Using ChatGPT & GPT-4 to generate CRAM & PyCRAM designators in a one-shot fashion

Tool for copying read-alignments regions centered around variants (in VCF/VCF.GZ/BCF format) from existing genomes (in SAM/BAM/CRAM format) to insert them into canvas genomes (in SAM/BAM/CRAM format).

Machinekit configuration for the Fabrikator Mini + CRAMPS board

A script to report depth of coverage from BAM/SAM/CRAM file or parse the output generated from "samtools depth"

Tool for adding genomic variants to an existing genome (in SAM/BAM/CRAM format). Currently supported variants are SNVs, indels and SVs (insertions, deletions, translocations, inversions and duplications). It generates realistic genomes as almost always less than 99% of the original real genome is modified.