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fastq

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OpenGene /fastp

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

adapter quality bioinformatics quality-control filter ngs sequencing overlap splitting duplication umi trimming preprocessing filtering illumina fastq merging qc polyg

UpdatedNov 28, 2024
C++

shenwei356 /seqkit

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

golang bioinformatics cross-platform tool toolkit fasta manipulation sequence fastq

UpdatedMar 14, 2025
Go

torognes /vsearch

Versatile open-source tool for microbiome analysis

search bioinformatics clustering metagenomics chimera fasta microbiome fastq metabarcoding amplicon sequence-alignment

UpdatedMar 11, 2025
C++

seqan3

seqan /seqan3

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

bioinformatics modern fasta blast seqan fastq samtools sequence-alignment fm-index sequence-analysis cpp20 cpp-concepts

UpdatedMar 16, 2025
C++

sdparekh /zUMIs

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

rna-seq pipeline expression rnaseq umi single-cell fastq barcodes dge

UpdatedJul 12, 2024
R

lmdu /pyfastx

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

python bioinformatics genome biology assembly dna fasta sequence fastq

UpdatedDec 26, 2024
C

mbhall88 /rasusa

Randomly subsample sequencing reads or alignments

rust coverage bioinformatics random alignment fasta bam fastq genome-analysis downsample subsampling

UpdatedNov 29, 2024
Rust

OpenGene /AfterQC

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

bioinformatics quality-control ngs sequencing overlap error trimming filtering fastq qc adapter-trimming

UpdatedMay 14, 2020
Python

genomics

igordot /genomics

A collection of scripts and notes related to genomics and bioinformatics

science workflow bioinformatics nanopore genomics sequencing vcf dna fasta gtf illumina fastq fast5

UpdatedFeb 10, 2025
R

broadinstitute /viral-ngs

Viral genomics analysis pipelines

genomics genome variant-calling bam genome-sequencing illumina fastq genome-assembly variant-annotations viral-ngs viral

UpdatedSep 20, 2024
Python

nf-core /fetchngs

Pipeline to fetch metadata and raw FastQ files from public databases

workflow pipeline nextflow download geo fastq synapse sra ena nf-core ddbj

UpdatedMar 13, 2025
Nextflow

Genetalks /gtz

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

gene compression nanopore sam pacbio compress bam fastq genomic-data-compression compression-rate fastq-compression gtx

UpdatedApr 18, 2022

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

compression gzip genomics sam vcf fasta bam fastq gvf samtools bwa 23andme cram bgzip

UpdatedFeb 27, 2025
C

seq2science

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.

bioinformatics rna-seq snakemake pipeline reproducible-research ngs bioinformatics-pipeline chip-seq atac-seq workflows fastq sra

UpdatedFeb 5, 2024
Python

OpenGene /MutScan

Detect and visualize target mutations by scanning FastQ files directly

visualization bioinformatics validation cancer detection ngs mutation variant fastq somatic

UpdatedFeb 10, 2022
C

ngless-toolkit /ngless

NGLess: NGS with less work

science haskell bioinformatics genomics ngs next-generation-sequencing metagenomics bioinformatics-pipeline fastq-format fastq haskell-language samtools bwa

UpdatedAug 13, 2024
Haskell

tseemann /nullarbor

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

public-health report variant-calling bacteria fastq phylogenomics denovo-assembly genotyping resistome virulome

UpdatedMar 19, 2024
Perl

alastair-droop /fqtools

An efficient FASTQ manipulation suite

bioinformatics next-generation-sequencing fastq fastq-files

UpdatedJan 27, 2020
C

seqfu2

telatin /seqfu2

🚀 seqfu - Sequece Fastx Utilities

bioinformatics genomics ngs sequencing bioconda fasta fastq bioinformatics-tool

UpdatedJan 20, 2025
Nim

labsquare /FastQt

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

gui bioinformatics qt5 fastq-format fastq

UpdatedAug 4, 2020
C++

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