Benchmark and toy datasets

An extremely fast Python package and project manager, written in Rust.

UPHL's Reference Free Pipeline

post processing of bacterial pangenome gene presence/absence matrices

chuckle-cli is a command-line application that utilises an API in order to print out jokes in your terminal

GitHub Action to build and push Docker images with Buildx

A tool for generating consensus long-read assemblies for bacterial genomes

SEER, reimplemented in python 🐍🔮

A k-mer-based maximum likelihood method for estimating distances of reads to genomes and phylogenetic placement.

Tools for working with SAM/BAM data

a Bioinformatics Application for Navigating De novo Assembly Graphs Easily

kmer based single-nucleotide polymorphism analysis

HoCoRT - Remove specific organisms from sequencing reads

HMMER: biological sequence analysis using profile HMMs

FLASH (Fast Length Adjustment of SHort reads); mirror of https://git.code.sf.net/p/flashpage/code

FastTree 2: Approximately-Maximum-Likelihood Trees for Large Alignments

A clone of http://www.clustal.org/omega

MitoFinder: efficient automated large-scale extraction of mitogenomic data from high throughput sequencing data

A collection of scripts to assist in the retrieval of data from the ENA Browser

Variant calling pipeline designed for Q20+ ONT long-reads

A nextflow pipeline that accommodates different sequencing technologies (Illumina or Nanopore), sample types (clinical or wastewater), and viral targets (Influenza or RSV).

⚙️🗑️ A GitHub Action to free disk space on an Ubuntu runner.

Bash script to download/update snapshots of files from NCBI genomes repository (refseq/genbank) with track of changes and without redundancy

Web application to explore the Sequence Read Archive.