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abricate

:mag_right: :pill: Mass screening of contigs for antimicrobial and virulence genes

bio-it-scripts

biocode

Bioinformatics code libraries and scripts

bioinformatics-one-liners

Bioinformatics one liners from Ming Tang

edirectcookbook

fastani

Fast Whole-Genome Similarity (ANI) Estimation

homoplasyfinder

A tool to identify and annotate homoplasies on a phylogeny and sequence alignment

kraken_db_install_scripts

Updated Kraken DB install scripts to cope with new-ish NCBI structure

legen_pipeline

Lactobacillus Evolutionary Genomics Pipeline

mrbayes

MrBayes is a program for Bayesian inference and model choice across a wide range of phylogenetic and evolutionary models. For documentation and downloading the program, please see the home page:

nanostat

Create statistic summary of an Oxford Nanopore read dataset

ncbi-genome-download

Scripts to download genomes from the NCBI FTP servers

pgap

NCBI Prokaryotic Genome Annotation Pipeline

proclasp

Classification of prokaryotic genomes on the species level

progenomics

A toolkit for prokaryotic comparative genomics

qiime

Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.

shivgami

SHIVGAMI is a tool, which run blastX process by assembling the CPU cores from avaialble Linux computing units.

spades

SPAdes Genome Assembler

tidytypes

Functions to Download Type Strain Names

to-gff

Convert .gbk or .embl to .gff (and optionally .fa) (required for QUAST)