fastq

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

A cross-platform and ultrafast toolkit for FASTA/Q file manipulation

Versatile open-source tool for microbiome analysis

The modern C++ library for sequence analysis. Contains version 3 of the library and API docs.

Easier download/extract of FASTA/Q read data and metadata from the ENA, NCBI, AWS or GCP.

a python package for fast random access to sequences from plain and gzipped FASTA/Q files

zUMIs: A fast and flexible pipeline to process RNA sequencing data with UMIs

Randomly subsample sequencing reads or alignments

A collection of scripts and notes related to genomics and bioinformatics

Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

Pipeline to fetch metadata and raw FastQ files from public databases

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

A modern compressor for genomic files (FASTQ, SAM/BAM/CRAM, VCF, FASTA, GFF/GTF/GVF, 23andMe...), up to 5x better than gzip and faster too

A high performance and compression ratio compressor for genomic data, powered by GTXLab of Genetalks.

Automated and customizable preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and (sc)RNA-seq workflows. Works equally easy with public as local data.

Detect and visualize target mutations by scanning FastQ files directly

NGLess: NGS with less work

💾 📃 "Reads to report" for public health and clinical microbiology

An efficient FASTQ manipulation suite

🚀 seqfu - Sequece Fastx Utilities