In silico serotype prediction for Listeria monocytogenes

In silico prediction of E. coli serotype, pathotype and shiga toxin subtyping

Useful bash one-liners for bioinformatics.

Comprehensive list of color palettes available in R ❤️🧡💛💚💙💜

VCF-kit: Assorted utilities for the variant call format

This repository is a cloud storage of my new research ideas and interests in Bioinformatics and Computational Biology. Github is a good way to keep tracks the improvements of a generalized works in…

Fast, robust ANI and aligned fraction for (metagenomic) genomes and contigs.

Tutorials on phylogenetic and phylogenomic inference

Efficient phylogenetic tree inference for massive taxonomic datasets

🌱 ➡️ 🌳 Add new taxa or taxonomic groups to the NCBI Taxdump files

Frequently used commands in bioinformatics

Python package for detection of chimerism and contamination in prokaryotic genomes.

a collection of scripts for organising bacterial genomes by species

a tool to filter sites in a FASTA-format whole-genome pseudo-alignment

A tool for removing redundant genomes from a set of assemblies

GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

Get microbial sequence data easier and faster

CGView is a Java package for generating high-quality, zoomable maps of circular genomes.

Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets

A practical cross-platform command-line tool for safely batch renaming files/directories via regular expression

Rename files in bulk.

A collection of guidelines for writing file names used in web projects.

Rapid determination of appropriate reference genomes.

A grammar of graphics for comparative genomics

Simple utility to concatenate .fastq(.gz) files whilst creating a summary of the sequences.

Awesome resources on Bioinformatics, data science, machine learning, programming language (Python, Golang, R, Perl) and miscellaneous stuff.

A cross-platform, efficient and practical CSV/TSV toolkit in Golang

Accurate metagenomic profiling && Fast large-scale sequence/genome searching

Pairwise SNP distance matrix from a FASTA sequence alignment