Command-line JSON processor

A versatile pairwise aligner for genomic and spliced nucleotide sequences

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

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

Toolkit for processing sequences in FASTA/Q formats

bedtools - the swiss army knife for genome arithmetic

De novo assembler for single molecule sequencing reads using repeat graphs

This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html

Prodigal Gene Prediction Software

Align proteins to genomes with splicing and frameshift

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

Short read de novo assembler using de Bruijn graphs, as published in: D.R. Zerbino and E. Birney. 2008. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Research, 1…

Finds SNP sites from a multi-FASTA alignment file

Fast and accurately polish the genome generated by long reads.

Robinhood Policy Engine : a versatile tool to monitor filesystem contents and schedule actions on filesystem entries.

Constructing a pangenome gene graph

A tool set for short variant discovery in genetic sequence data.

Simple oligo analysis and primer design

A genomic k-mer counter (and sequence utility) with nice features.

Pairwise SNP distance matrix from a FASTA sequence alignment

De novo genome assembly and multisample variant calling

a python package for finding tandem repeats from genomic sequences

Calculate confidence scores from Kraken2 output

Rapidly extract a flexible bacterial core genome alignment