What should perfect bioinformatic tools be like?

plotthis is an R package that is built upon ggplot2 and other plotting packages.

My tools for the Slurm HPC workload manager

Scalable annotated de Bruijn graphs for DNA indexing, alignment, and assembly

Assembly topology from long-read alignments

ShinkaEvolve: Towards Open-Ended and Sample-Efficient Program Evolution

A script to convert WHO MTB resistant variants to a format that can be ingested by TBProfiler

Phylogenetic alignment parlor game

Ansible playbooks and configuration of infrastructure on an existing OpenStack cloud

nextflow for tb pipeline

Kayobe configuration for the Kayobe workshop "A Universe from Nothing: Containerised OpenStack deployment using Kolla, Ansible and Kayobe"

ultrafast taxonomic profiling and genome querying for metagenomic samples by abundance-corrected minhash.

🚀 seqfu - Sequece Fastx Utilities

The AMRgen package provides tools for interpreting antimicrobial resistance (AMR) genes, integrating genomic data with phenotypic antimicrobial susceptibility testing (AST) data, and calculating ge…

Create phylogenetic trees from Bracken/Kraken2 reports

Drug Resistance Prediction with Reference Graphs

Web application to explore the Sequence Read Archive.

Mycobacterium tuberculosis mixture detection and strain typing from WGS data

Code used for WHO analysis work

Mycobacterium tuberculosis complex lineage typing

Gotree is a set of command line tools and an API to manipulate phylogenetic trees. It is implemented in Go language.

Goalign is a set of command line tools and an API to manipulate multiple sequence alignments. It is implemented in Go language.

A fast approximate aligner for long DNA sequences

Mycobacterial pipeline

COBS - Compact Bit-Sliced Signature Index (for Genomic k-Mer Data or q-Grams)

BItsliced Genomic Signature Index - Efficient indexing and search in very large collections of WGS data