SPAdes Genome Assembler

Java utilities for Bioinformatics

Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing

A curated list of resources for learning bioinformatics.

Rapid large-scale prokaryote pan genome analysis

NGMLR is a long-read mapper designed to align PacBio or Oxford Nanopore (standard and ultra-long) to a reference genome with a focus on reads that span structural variations

Fast taxonomic classification of metagenomic sequencing reads using a protein reference database

Finds SNP sites from a multi-FASTA alignment file

Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation

Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement

A tool to circularize genome assemblies

Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins

Antimicrobial Resistance Identification By Assembly

NGLess: NGS with less work

Rare variant test software for next generation sequencing data

An efficient FASTQ manipulation suite

MrBiomics: Composable modules and recipes automate bioinformatics for multi-omics analyses

Detect germline or somatic variants from normal or tumour/normal whole-genome or targeted sequencing

Get assembly statistics from FASTA and FASTQ files

Program for estimating πN/πS, dN/dS, and other diversity measures from next-generation sequencing data