illumina

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

Viral genomics analysis pipelines

A collection of scripts and notes related to genomics and bioinformatics

Amplicon sequencing analysis workflow using DADA2 and QIIME2

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

Aligns short reads using dynamic seed size with strobemers

An accurate and ultra-fast hybrid genome assembler

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

Analysis pipelines for genomic sequencing data

A permissively licensed library designed to replace Illumina's Experiment Manager

Command line utility for manipulating Illumina-generated FastQ files.

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

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

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

Please switch to https://github.com/OpenGene/defastq

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

A collection of publications on comparison of high-throughput sequencing technologies.

(No maintenance) Next Generation Sequencing Simulation with SNP, Variation and Sequencing Error Integrated

CheckQC inspects the content of an Illumina runfolder and determines if it passes a set of quality criteria

Fast-SG: An alignment-free algorithm for ultrafast scaffolding graph construction from short or long reads.