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

SPAdes Genome Assembler

Clair3 - Symphonizing pileup and full-alignment for deep learning-based long-read variant calling

Amplicon sequencing analysis workflow using DADA2 and QIIME2

A collection of scripts and notes related to genomics and bioinformatics

viral-ngs: command line tools and wrappers for processing raw viral genomic data

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

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

Command line utility for manipulating Illumina-generated FASTQ files.

An accurate and ultra-fast hybrid genome assembler

Scripts, utilities and programs for genomic bioinformatics.

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

Demultiplexing pipeline for sequencing data

Parse Illumina sample sheets with Python

Design degenerated primers on highly variable alignments for full genome sequencing or qPCR. Specifically developed for viruses.

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

16S rDNA V3-V4 amplicon sequencing analysis using dada2, phyloseq, LEfSe, picrust2 and other tools. Demo: https://ycl6.github.io/16S-Demo/

An accurate and ultra-fast adapter and quality trimming program for Illumina Next-Generation Sequencing (NGS) data.

Explore and download data from the recount3 project

A Nextflow workflow for QC, evaluation, and profiling of metagenomic samples using short- and long-read technologies

Mapping-based Genome Size Estimation (MGSE) performs an estimation of a genome size based on a read mapping to an existing genome sequence assembly.

A pipeline to detect chimeric transcripts derived from genes and transposable elements.

A pipeline for preprocessing NGS data from Illumina, Nanopore and PacBio technologies

A Snakemake workflow to process single samples or cohorts of Illumina paired-end sequencing data (WGS or WES) using trim galore/bwa/GATK4/parabricks.