oschwengers

bakta

Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

platon

Identification & characterization of bacterial plasmid-borne contigs from short-read draft assemblies.

referenceseeker

Rapid determination of appropriate reference genomes.

asap

A scalable bacterial genome assembly, annotation and analysis pipeline

tadrep

Targeted Detection and Reconstruction of Plasmids

ANIclustermap

A tool for drawing ANI clustermap between all-vs-all microbial genomes using fastANI & seaborn

Awesome-Bioinformatics

A curated list of awesome Bioinformatics libraries and software.

bakHEAT

Visualize microbial evolution at the SNP level!

MGCplotter

Microbial Genome Circular plotting tool using Circos

mummer2circos

Circular bacterial genome plots based on BLAST or NUCMER/PROMER alignments

py_nf

Python library to execute batches of jobs using nextflow.

academicpages.github.io

Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes

apiad.github.io

Personal website, portfolio, blog and brain dumpster.

bacteria-archaea-traits

A synthesis of bacterial and archaeal phenotypic trait data

bioconda-recipes

Conda recipes for the bioconda channel.

biopython

Official git repository for Biopython (originally converted from CVS)

deep-rules

Ten Quick Tips for Deep Learning in Biology

deepsig

DeepSig - Predictor of signal peptides in proteins based on deep learning

ESCMID-MGE-2022

homebrew-bio

:beer::microscope: Bioinformatics formulae for the Homebrew package manager (macOS and Linux)

hybracter

Automated long-read first bacterial genome assembly pipeline implemented in Snakemake using Snaketool.

Macsyfinder_models

Repository containing up-to-date definitions and models for the detection of macromolecular systems with MacSyFinder.

microbiome-bioinformatics

Jekyll Template - Mediumish

modules

Repository to host tool-specific module files for the Nextflow DSL2 community!

oschwengers

staged-recipes

A place to submit conda recipes before they become fully fledged conda-forge feedstocks

tools-iuc

Tool Shed repositories maintained by the Intergalactic Utilities Commission

training-collection

Collection of bioinformatics training materials

unishox2-py3

A package for Unicode-friendly string compression using Unishox2

zDB

zDB: comparative bacterial genomics made easy