SPAdes Genome Assembler
Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
Java utilities for Bioinformatics
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
MrBiomics: Composable modules and recipes automate bioinformatics for multi-omics analyses
NGLess: NGS with less work
Rare variant test software for next generation sequencing data
An efficient FASTQ manipulation suite
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
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