pybedtools

automlsa2

Automated Multi-Locus Sequence Analysis phylogenetic tree construction software

bs3

BS-Seeker3: An Ultra-fast, Versatile Pipeline for Mapping Bisulfite-treated Reads.

biopython

Official git repository for Biopython (originally converted from CVS)

demuxalot

Reliable, scalable, efficient demultiplexing for single-cell RNA sequencing

crispy

Python module to analyse CRISPR-based libraries

genomepy

genes and genomes at your fingertips

genomics-data-index

Indexes genomes using SNVs, MLST, or kmers for rapid querying, clustering, and visualization.

gffutils

GFF and GTF file manipulation and interconversion

metaseq

Framework for integrated analysis and plotting of ChIP/RIP/RNA/*-seq data

bakta

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

pca-on-genotypes

ngs-tools

Miscellaneous tools for genomics

referenceseeker

Rapid determination of appropriate reference genomes.

binf-scripts

A collection of useful bioinformatics scripts.

tadrep

Targeted Detection and Reconstruction of Plasmids