There are 9 repositories under fastq topic.
A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
Viral genomics analysis pipelines
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.
NGLess: NGS with less work
An efficient FASTQ manipulation suite
Command line utility for manipulating Illumina-generated FASTQ files.
Detecting contamination in NGS data and multi-species analysis
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.
Nucleotide Archival Format - Compressed file format for DNA/RNA/protein sequences
Exome/Capture/RNASeq Pipeline Implementation using snakemake
Fast FASTA/Q parser and writer (C++ re-implementation of kseq library)