Machinekit configuration for the Fabrikator Mini + CRAMPS board

a REST service to launch pipeline

Line cramming/un-cramming utility

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

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

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

an API for intersections of genomic data

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

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

Frequently used commands in bioinformatics

Fast and accurate sequence demultiplexing

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

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.

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).

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

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

Functional tests for command line applications

Rust software for solving impartial games.

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

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