clintval

sample-sheet

Parse Illumina sample sheets with Python

genome-browser

A lightweight Python graphing API for genomic features

nucleic

Analysis and plotting library for base substitution spectra and signatures

krakenplot

🦑 Visualize phylogenetic trees from the taxonomic sequence classifier Kraken

bimap

A modern bidirectional map in Scala

bwa

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

commons

Common scala utilities

fgbio

Tools for working with genomic and high throughput sequencing data.

htsjdk

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

caseless

A typed dictionary in Python with case-insensitive keys

fullypeek

Peek forward in a Rust iterator as far as you'd like, memory allowing!

conda-forge-pinning-feedstock

A conda-smithy repository for conda-forge-pinning.

dataclass-csv

Map CSV to Data Classes

dotenv-java

🗝️ Dotenv is a no-dep, pure Java module that loads environment variables from a .env file

example-plugin

A miniature example of a MultiQC plugin.

fullypeekable

Peek forward in a Scala iterator as far as you'd like, memory allowing!

groupingiterator

homebrew-core

🍻 Default formulae for the missing package manager for macOS (or Linux)

homebrew-verticalize

manta

Structural variant and indel caller for mapped sequencing data

monoclparse

Parse Monocl Excel business report documents and intersect them!

MultiQC

Aggregate results from bioinformatics analyses across many samples into a single report.

picard

A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

plugins

Nextflow plugins index repository

pysam

Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.

quald

Detect the quality encoding of FASTQ files using Rust

samplesheet

A permissively licensed library designed to replace Illumina's Experiment Manager.

staged-recipes

A place to submit conda recipes before they become fully fledged conda-forge feedstocks

VarDictJava

VarDict Java port

verticalize

Simple tool to verticalize text delimited files.