A web-based collaborative LaTeX editor

An LLM-powered knowledge curation system that researches a topic and generates a full-length report with citations.

snipit: summarise snps relative to your reference sequence

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

NCBI-style taxdump files for International Committee on Taxonomy of Viruses (ICTV)

A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

customizable pipeline to identify viral sequences from (meta)genomic data

geNomad: Identification of mobile genetic elements

Tools for working with SAM/BAM data

A Python package for obtaining complete lineages and the lowest common ancestor (LCA) from a set of taxonomic identifiers

The next version of bwa-mem

A fast and sensitive gapped read aligner

Read alignment statistics for metagenomics

An R package designed for drawing gene arrow maps

A grammar of graphics for comparative genomics

a Bioinformatics Application for Navigating De novo Assembly Graphs Easily

viralVerify: viral contig verification tool

VirBot: a protein-based RNA virus detector for metagenomic data

SPAdes Genome Assembler

Ultra-fast and memory-efficient (meta-)genome assembler

Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

Tools (written in C using htslib) for manipulating next-generation sequencing data

Spliced read mapper for RNA-Seq

RNA-seq aligner

Aggregate results from bioinformatics analyses across many samples into a single report.

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

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

Genome assembly evaluation tool

Accelerated BLAST compatible local sequence aligner.