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ariba

Antimicrobial Resistance Identification By Assembly

brucella_vf

:mag_right: :pill: Mass screening of contigs for brucella virulence genes

cossa-workflows

CoSSA (Prodhomme et al., 2019) is a set of workflows used to identify quickly and efficiently haplotype specific SNPs linked to a trait of interest from Whole Genome Sequencing data. All the contributors to the design of these workflows are Danny Esselink, Charlotte Prodhomme and Theo Borm (Wageningen University UR Plant Breeding).

deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

microbiome_helper

A repository of bioinformatic scripts, SOPs, and tutorials for analyzing microbiome data.

ml-for-beginners

12 weeks, 24 lessons, classic Machine Learning for all

pan-genome-visualization

pangenomealignmentgenerator

Align SRAs to pangenome FASTA file generated by Roary

python-100-days

Python - 100天从新手到大师

regression-power

Power Regression

roary

Rapid large-scale prokaryote pan genome analysis

snippy

:scissors: :zap: Rapid haploid variant calling and core genome alignment

snp-sites

Finds SNP sites from a multi-FASTA alignment file

tutorials

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!

wikiq

an xml to .tsv converter for wikimedia XML data dumps