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anvio

An analysis and visualization platform for 'omics data

apod-api

Astronomy Picture of the Day API service

bio-tradis

A set of tools to analyse the output from TraDIS analyses

bio_scripts

Practical, reusable scripts for bioinformatics

bioinformatics-workbook

chewbbaca

BSR-Based Allele Calling Algorithm

chewbbaca_tutorial

Step by step tutorial using chewBBACA with all necessary files and results

clermontyping

Clermont PCR method In-Silico

clinker

Gene cluster comparison figure generator

coreuscan

A tool for downloading Core Genome MLST schemes for bacterial genomics for use with chewBBACA

datacarpentry.github.io

Website repo

genomics

a collection of scripts and notes related to genomics and bioinformatics

ggplot2

An implementation of the Grammar of Graphics in R

gotree

Gotree

itolapi

Python API for the Interactive Tree of Life (iTOL)

ls-bsr

Large scale Blast Score Ratio (BSR) analysis

mentalist

The MLST pipeline developed by the PathOGiST research group

minced

Mining CRISPRs in Environmental Datasets

ncbi-genome-download

Scripts to download genomes from the NCBI FTP servers

ndafp

New version

padloc-db

HMMs and system models used by PADLOC

pavian

🌈 Interactive analysis of metagenomics data

phispy

Prediction of prophages from bacterial genomes

plasflow

Software for prediction of plasmid sequences in metagenomic assemblies

prodigal_training_files

species specific training files based on specific reference genomes

public-apis

A collective list of free APIs for use in software and web development.

r-ecology-lesson

:notebook: Data Carpentry R lessons on ecology.

roary

Rapid large-scale prokaryote pan genome analysis

seqmagick

An imagemagick-like frontend to Biopython SeqIO

srst2

Short Read Sequence Typing for Bacterial Pathogens