collection of tools for the analysis and cleaning of genome assemblies

Tip and tricks for R

The BV-BRC Command Line Interface

A demonstration of public database API queries and data organisation.

Machine Learning Experiments and Work

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

Using ggtree to build phylogenetic trees

Bayesian haplotype-based genetic polymorphism discovery and genotyping.

Bifrost graph gene caller.

Statistics course for JHU Genomic Data Science Sequence

What the f*ck Python? 😱

Notebook and raw data reconciling UK and AAFC Enterococcus metadata with deposited and used data

NCBI Prokaryotic Genome Annotation Pipeline

Gene cluster comparison figure generator

The new Sanger Pathogen Informatics RNA Seq analysis pipeline

The next version of bwa-mem

Code and analyses for ASM msystems paper.

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!

Code repository for machine learning and computational analysis of large-scale microbial genomics data (https://rdcu.be/9rHj)

Learn interpretable computational phenotyping models from k-merized genomic data

⚡ ♒ Rapid prokaryotic genome annotation

Rapid large-scale prokaryote pan genome analysis

Resistance Gene Identifier (RGI). Software to predict resistomes from protein or nucleotide data, including metagenomics data, based on homology and SNP models.

A fast multi-threaded k-mer counter

Fast and frugal disk based k-mer counter

Course materials for the Data Science Specialization: https://www.coursera.org/specialization/jhudatascience/1