Stars
Python script for downloading assemblies from enterobase
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
HCGB-IGTP / spaTyper
Forked from mjsull/spa_typingComputational method for finding spa types.
Archived - please see updated sccmec tool at link below
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