Rapid & standardized annotation of bacterial genomes, MAGs & plasmids

🆔 Scan contig files against PubMLST typing schemes

dN/dS methods to quantify selection in cancer and somatic evolution

Scalable Set Visualization using Hierarchies

Source code for the crAssphage project

Fast genome-wide functional annotation through orthology assignment

SPAdes Genome Assembler

Within-species genome-wide dN/dS estimation from very many genomes

✂️ ⚡ Rapid haploid variant calling and core genome alignment

Clermont PCR method In-Silico

All scripts used for the analysis of the twilight of the pan-genome, and scripts available for others to apply similar analysis

DataViz protocols book for wet lab scientists

Predicting plasmid contigs from assemblies using single copy marker genes, plasmid genes, kmers - Developed by Linda van der Graaf

MetaSIPSim: A tool for simulating metagenomic-SIP read libraries

Plascad is a computationally efficient tool designed for plasmids classification, antibiotic resistance genes (ARGs) annotation and plasmid visualization.

MetaMLST is a computational tool for in-silico Multi-Locus Sequence Typing from metagenomic data.

pipeline for read mapping, snp calling and annotation for bacterial genomes

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

Workflow for secondary metabolite biosynthetic gene clusters comparison and pangenome mining

Contains a fasta format database of a large variety of mobile genetic elements and an annotation file

Microbial Populations as Clusters Of Gene Transfer

In this repo you will find demos and tutorials prepared by members of the CBIB. Feel free to use them for non-commercial activities given that you give proper credit. Have fun!

A simple gene co-expression analyses workflow powered by tidyverse and graph analyses