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

SortMeRNA: next-generation sequence filtering and alignment tool

UGENE is free open-source cross-platform bioinformatics software

Rare variant test software for next generation sequencing data

BWA-MEME: Faster BWA-MEM2 using learned-index

TPMCalculator quantifies mRNA abundance directly from the alignments by parsing BAM files

Generate duplex/single consensus reads to reduce sequencing noises and remove duplications

An ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data. This tool can be used to detect viral infectious diseases, like COVID-19.

A method for variant graph genotyping based on exact alignment of k-mers

Scalable long read self-correction and assembly polishing with multiple sequence alignment

Calculation of pairwise Linkage Disequilibrium (LD) under a probabilistic framework

Ococo: the first online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream.

Improving gene isoform quantification with miniQuant

Method to optimally select samples for validation and resequencing

Ultrafast sequence typing and gene detection from NGS raw reads

FQSqueezer - FASTQ compressor based on k-mer statistics

A modernized ART for Illumina read simulation.

Estimation of per-individual inbreeding tracts under a probabilistic framework

Official code repository for JAX-CNV

Hybrid method based on a variable-order de bruijn Graph for the error Correction of Long Reads