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manta

Structural variant and indel caller for mapped sequencing data

matplotlib

matplotlib: plotting with Python

mill

Your shiny new Java/Scala build tool!

mkdocs-material

A Material Design theme for MkDocs

monoclparse

Parse Monocl Excel business report documents and intersect them!

mpl-helpers

Matplotlib wrappers for those hard-to-remember figure tweaks.

mutpos2vcf

Script to convert Duplex Sequencing .mutpos file formats into valid VCF files

nucleic

Analysis and plotting library for base substitution spectra and signatures

og-equity-compensation

Stock options, RSUs, taxes — read the latest edition: www.holloway.com/ec

pendant

Python 3.6+ library for submitting to AWS Batch interactively

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.

progfun-wiki

refgene-parser

Quickly parse genes and exons from a RefGene file

rust-bio-tools

A set of command line utilities based on Rust-Bio.

sample-sheet

Parse Illumina sample sheets with Python

samplesheet

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

scikit-bio

scikit-bio is an open-source, BSD-licensed, Python package providing data structures, algorithms, and educational resources for bioinformatics.

seattle-food-truck

Python app for the glorious food trucks in Seattle 🌭

smart_open

Utils for streaming large files (S3, HDFS, gzip, bz2...)

snakescale

Non-strict wrappers for the data pipelining language Snakemake

snpeff

snpsift

sopt

An argument parsing library for Scala

starfish

Intersect multiple VCF files with haplotype awareness

statsmodels

Statsmodels: statistical modeling and econometrics in Python

toygene

A minimalist alignment plotting library using toyplot graphs

vardict

VarDict

vardictjava

VarDict Java port

vartovcf

Convert variants from VarDict/VarDictJava into VCF v4.2 format.