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abricate

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

ace2

Supporting material and code for primate ACE2 project

alitv

Visualize whole genome alignments as linear maps

asqcan

Pipeline for bacterial genome assembly, quality control and annotation

bactdating

Bayesian inference of ancestral dates on bacterial phylogenetic trees

base_changer

Changes bases in a fasta file at user specified positions

bracken

Bracken (Bayesian Reestimation of Abundance with KrakEN) is a highly accurate statistical method that computes the abundance of species in DNA sequences from a metagenomics sample.

clonalframeml

ClonalFrameML: Efficient Inference of Recombination in Whole Bacterial Genomes

clusterdbanalysis

ITEP - Integrated Toolkit for Exploration of microbial Pan-genomes

comparative_genomics

Micro 612 genomics workshop

deviate

Python tool for the analysis and visualization of mobile genetic elements

environmental_cholera_haiti

Evidence of Environmental Evolution of Toxigenic Vibrio cholerae in Aquatic Reservoirs

fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

gotree

Gotree

imgeins

isquest

ISQuest

kaiju

Fast taxonomic classification of metagenomic sequencing reads using a protein reference database

king_et_al_2019

Script(s) used in publication of King et al, 2019 "A new high throughput sequencing assay for characterising the diversity of natural Vibrio communities and its application to a Pacific oyster mortality event"

linux-magic-trackpad-2-driver

mgefinder

A toolbox for identifying mobile genetic element (MGE) insertions from short-read sequencing data of bacterial isolates.

mgert

Mobile Genetic Elements Retrieving Tool

modeltest

Best-fit model selection

mustache

A flexible tool to identify mobile genetic elements and their sites of insertions from short-read whole-genome sequencing data.

pathogen-informatics-training

pop_gen

Population genetic scripts

public

Short scripts used for Assembly and Annotation

pysca

A python implementation of the Statistical Coupling Analysis (SCA)

ragoo

Fast Reference-Guided Scaffolding of Genome Assembly Contigs. RagTag, the successor to RaGOO, is now available here: https://github.com/malonge/RagTag

ragtag

A fast reference-guided genome assembly scaffolder

roary

Rapid large-scale prokaryote pan genome analysis