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OpenGene /fastp

Star2k

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++

ablab /spades

Star798

SPAdes Genome Assembler

sequencing next-generation-sequencing illumina genome-assembly sequence-assembler transcriptome-assembly metagenome-assembly

UpdatedMar 11, 2025
C++

HKU-BAL /Clair3

Star268

Clair3 - Symphonizing pileup and full-alignment for high-performance long-read variant calling

deep-learning nanopore genomics computational-biology pacbio variant-calling illumina long-reads variant-detection ont-data ont-models

UpdatedFeb 28, 2025
Python

igordot /genomics

Star206

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

nf-core /ampliseq

Star194

Amplicon sequencing analysis workflow using DADA2 and QIIME2

workflow pipeline nextflow metagenomics pacbio edna microbiome iontorrent illumina metabarcoding 16s rrna its 18s taxonomic-classification amplicon-sequencing qiime2 nf-core taxonomic-profiling

UpdatedMar 12, 2025
Nextflow

broadinstitute /viral-ngs

Star192

Viral genomics analysis pipelines

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

UpdatedSep 20, 2024
Python

ksahlin /strobealign

Star165

Aligns short reads using dynamic seed size with strobemers

bioinformatics alignment illumina short-read-mapping strobemers

UpdatedMar 18, 2025
C++

nf-core /taxprofiler

Star138

Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data

workflow bioinformatics nanopore pipeline nextflow shotgun pathogen metagenomics classification profiling microbiome illumina long-reads taxonomic-classification nf-core taxonomic-profiling

UpdatedMar 13, 2025
Nextflow

nf-core /viralrecon

Star133

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

workflow nanopore virus pipeline nextflow assembly metagenomics variant-calling illumina oxford-nanopore amplicon viral ont nf-core long-read-sequencing artic covid-19 covid19 sars-cov-2

UpdatedJan 27, 2025
Nextflow

parklab /xTea

Star107

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

nanopore pacbio illumina transposable-elements linked-reads mobile-element-insertion

UpdatedFeb 18, 2025
Python

stjude-rust-labs /fq

Star83

Command line utility for manipulating Illumina-generated FASTQ files.

rust bioinformatics genomics next-generation-sequencing illumina fastq fastq-files

UpdatedFeb 28, 2025
Rust

adigenova /wengan

Star83

An accurate and ultra-fast hybrid genome assembler

nanopore pacbio hybrid illumina genome-assembler

UpdatedApr 10, 2024
Perl

HKU-BAL /ClairS

Star81

ClairS - a deep-learning method for long-read somatic small variant calling

bioinformatics deep-learning nanopore genomics somatic-variants haplotypes pacbio somatic-mutations illumina indels phasing snvs long-reads ont long-read-sequencing short-reads

UpdatedFeb 27, 2025
Python

igordot /sns

Star66

Analysis pipelines for genomic sequencing data

bioinformatics rna-seq pipeline genomics analysis sequencing dna atac-seq wgs illumina wes wgbs rrbs nyu

UpdatedMar 17, 2025
Shell

0xTCG /aldy

Star62

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

bioinformatics sequencing illumina genotype adme pgrnseq cyp2d6 allele

UpdatedFeb 12, 2025
C

HKU-BAL /ClairS-TO

Star59

ClairS-TO - a deep-learning method for tumor-only somatic variant calling

bioinformatics deep-learning nanopore genomics somatic-variants variants pacbio variant-calling somatic-mutations illumina snvs long-reads ont long-read-sequencing tumors tumor-only

UpdatedMar 10, 2025
Python

fmalmeida /MpGAP

Star58

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

workflow nanopore pipeline nextflow reproducible-research reproducible-science pacbio polish illumina spades genome-assembly hybrid-assemblies unicycler flye canu pilon

UpdatedSep 9, 2024
Nextflow

clintval /sample-sheet

Star50

Parse Illumina sample sheets with Python

python bioinformatics illumina demultiplexing experiment-manager samplesheet

UpdatedMar 20, 2024
Python

nf-core /demultiplex

Star45

Demultiplexing pipeline for sequencing data

workflow pipeline nextflow illumina demultiplexing bcl2fastq nf-core bases2fastq elementbiosciences

UpdatedMar 6, 2025
Nextflow

leekgroup /recount

Star41

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

count gene r human rstats bioconductor rnaseq deseq2 illumina exon junction derfinder annotation-agnostic recount

UpdatedDec 12, 2024
R

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