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

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

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

Rust software for solving impartial games.

Functional tests for command line applications

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

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

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).

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.

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

Fast and accurate sequence demultiplexing

Frequently used commands in bioinformatics

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

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

an API for intersections of genomic data

Convert output from Cram (and some other tools) to TAP (Test Anything Protocol)

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

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