cram

C library for high-throughput sequencing data formats

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

Last-night exam-cram coach as a Claude Agent Skill: turns your slides, notes and past papers into a chaptered knowledge base + quiz bank, teaches only what's in your materials, and never fabricates (measured 100% out-of-scope abstention). Bilingual EN/中文 — the 期末极速备考 skill.

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

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

Frequently used commands in bioinformatics

Functional tests for command line applications

Identify which human reference genome was used to align a BAM/SAM/CRAM file

Fast and accurate sequence demultiplexing

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

Pure-Rust BAM/VCF/BCF depth, pileup, variants & stats with Python bindings — native Linux/macOS/Windows wheels, pysam-parity, no htslib.

Markdown specification testing — Cram-style CLI testing with persistent shell context, pattern matching, and snapshot updates