Python script for downloading assemblies from enterobase

Automated Phylogenomic Inference Pipeline

Finding regions of similarity between plasmids

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

A collection of scripts used in the following research paper: https://doi.org/10.1101/785212

Abracadabra, a spell of ancient origin, is our key to unlocking the enigmatic power concealed within the genomes of Acinetobacter baumannii.

A genotyping pipeline for Acinetobacter baumannii, presented proudly by a capybara

Repository for https://www.nature.com/articles/s41598-019-47758-5

This is the code repository for reproducing analyses in the paper: CRISPR-Cas systems are widespread accessory elements across bacterial and archaeal plasmids

An accurate and sensitive bacterial plasmid identification tool based on deep machine-learning of shared k-mers and genomic features.

Insertion sequences (Insertion Element) [https://en.wikipedia.org/wiki/Insertion_sequence] collected from ISfinder (https://isfinder.biotoul.fr/)

A genome visualization python package for comparative genomics

High accuracy RAG for answering questions from scientific documents with citations

HattCI is a hidden Markov model for attC site identification in DNA sequence described in Pereira et al. 2016 (doi:10.1089/cmb.2016.0024)

A k-mer based program for the identification of known plasmids from whole-genome sequencing reads

a collection of scripts for organising bacterial genomes by species

Inferring bacterial recombination rates from large-scale sequencing datasets.

Supplementary E. coli virulence associated genes, including etsABC, cdtABC (I, II, III, IV and V), papG (I, II and III), uclD, entA, sinH, f17b-A, f17b-G, clbS, plasmid-borne ompT, hlyF and mig14, …

MOB-suite: Software tools for clustering, reconstruction and typing of plasmids from draft assemblies

Computational method for finding spa types.

Archived - please see updated sccmec tool at link below

Bacterial RNASeq analysis pipeline

kegg enrichment analysis

fast phage annotation program

Miscellaneous Perl scripts from 20 years in microbial bioinformatics

CNV detection for prokaryote genomes using NGS sequencing data

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

Bacterial variants(structural variant and single nucleotide variant) calling pipeline by short read NGS data

PaperBLAST: find papers about a protein or its homologs