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fasterqc

A non-Java alternative to the classic FastQC tool

freebayes

Bayesian haplotype-based polymorphism discovery and genotyping.

fripan

Interactive, web tool for exploring pan-genome of bacterial strains

galaxy_wrappers

Repo for my galaxy wrappers and associated packages

gard

🍆 💊 Gonococcal Antimicrobial Resistance Detection

gbk2bcfgff

Convert Genbank to GFF compatible with "bcftools csq"

govaluate

Arbitrary expression evaluation for golang

graphaligner

heterik

Estimate heterozygosity or mixture level of a bacterial WGS sample

homebrew-bio

:beer::microscope: Bioinformatics formulae for the Homebrew and Linuxbrew package managers

homebrew-bioinformatics-linux

:beer: :penguin: Homebrew formulae for bioinformatics software only available for Linux

homebrew-core

🍻 Default formulae for the missing package manager for macOS

homebrew-extra

:candy::penguin: Linux-only formulae that are not dependencies of core formulae

homebrew-science

:snowflake: Scientific formulae for Homebrew and Linuxbrew (legacy)

injecta

Insert genes into genomes to aid synthetic test data generation

iupak

Decode and display IUPAC code information

joystx

Shigatoxin STX typing for E.coli STEC

kalign

A fast multiple sequence alignment program.

klosham

Find closest aligned sequences to a query sequnece

kopynumba

Identify copy number variation in bacterial Illumina sequences

kounta

🧮 🔢 Generate multi-sample k-mer count matrix from WGS

kroucha

Mock repository for Sanger publications citing Croucher et al

kurra

Fast whole genome phylogeny

lathe

A tool for generating bacterial genomes from metagenomes with nanopore long read sequencing

legsta

🍗⭐ In silico Legionella pneumophila Sequence Based Typing

linuxbrew-core

🍻🐧 Core formulae for the Homebrew package manager on Linux

mapcaller

MapCaller – An efficient and versatile approach for short-read alignment and variant detection in high-throughput sequenced genomes

mash

Fast genome and metagenome distance estimation using MinHash

mini-outbreak

Small WGS dataset for testing bacterial outbreak analysis pipelines

minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences