SPAdes Genome Assembler

Java utilities for Bioinformatics

A curated list of resources for learning bioinformatics.

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

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

A tool to circularize genome assemblies

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

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

Antimicrobial Resistance Identification By Assembly

NGLess: NGS with less work

An efficient FASTQ manipulation suite

Rare variant test software for next generation sequencing data

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

Microsatellite Instability (MSI) detection using high-throughput sequencing data.