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

SPAdes Genome Assembler

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

A collection of scripts and notes related to genomics and bioinformatics

Viral genomics analysis pipelines

Amplicon sequencing analysis workflow using DADA2 and QIIME2

Aligns short reads using dynamic seed size with strobemers

Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

Assembly and intrahost/low-frequency variant calling for viral samples

Comprehensive TE insertion identification with WGS/WES data from multiple sequencing technics

An accurate and ultra-fast hybrid genome assembler

Command line utility for manipulating Illumina-generated FASTQ files.

ClairS - a deep-learning method for long-read somatic small variant calling

Analysis pipelines for genomic sequencing data

Allelic decomposition and exact genotyping of highly polymorphic and structurally variant genes

Multi-platform genome assembly pipeline for Illumina, Nanopore and PacBio reads

ClairS-TO - a deep-learning method for tumor-only somatic variant calling

Parse Illumina sample sheets with Python

Demultiplexing pipeline for sequencing data

R package for the recount2 project. Documentation website: http://leekgroup.github.io/recount/