fastq

shenwei356/seqkit

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

torognes/vsearch

Versatile open-source tool for microbiome analysis

seqan/seqan3

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

sdparekh/zUMIs

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

lmdu/pyfastx

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

mbhall88/rasusa

Randomly subsample sequencing reads or alignments

OpenGene/AfterQC

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

igordot/genomics

A collection of scripts and notes related to genomics and bioinformatics

broadinstitute/viral-ngs

Viral genomics analysis pipelines

Genetalks/gtz

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

divonlan/genozip

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

vanheeringen-lab/seq2science

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.

nf-core/fetchngs

Pipeline to fetch metadata and raw FastQ files from public databases

OpenGene/MutScan

Detect and visualize target mutations by scanning FastQ files directly

ngless-toolkit/ngless

NGLess: NGS with less work

alastair-droop/fqtools

An efficient FASTQ manipulation suite

tseemann/nullarbor

:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology

telatin/seqfu2

:rocket: seqfu - Sequece Fastx Utilities

labsquare/FastQt

FastQC port to Qt5: A quality control tool for high throughput sequence data.

mdshw5/fastqp

Simple FASTQ quality assessment using Python

fulcrumgenomics/fqgrep

Grep for FASTQ files

chrovis/cljam

A DNA Sequence Alignment/Map (SAM) library for Clojure

stjude-rust-labs/fq

Command line utility for manipulating Illumina-generated FASTQ files.

markschl/seq_io

FASTA and FASTQ parsing in Rust

StevenWingett/FastQ-Screen

Detecting contamination in NGS data and multi-species analysis

Daniel-Liu-c0deb0t/UMICollapse

Accelerating the deduplication and collapsing process for reads with Unique Molecular Identifiers (UMI). Heavily optimized for scalability and orders of magnitude faster than a previous tool.

BioJulia/FASTX.jl

Parse and process FASTA and FASTQ formatted files of biological sequences.

muellan/metacache

memory efficient, fast & precise taxnomomic classification system for metagenomic read mapping

KirillKryukov/naf

Nucleotide Archival Format - Compressed file format for DNA/RNA/protein sequences

sbslee/fuc

Frequently used commands in bioinformatics

lgautier/fastq-and-furious

Efficient handling of FASTQ files from Python

aseyboldt/fastq-rs

lpryszcz/bin

My bioinfo toolbox

cartoonist/kseqpp

Fast FASTA/Q parser and writer (C++ re-implementation of kseq library)

patidarr/ngs_pipeline

Exome/Capture/RNASeq Pipeline Implementation using snakemake