Alternatives and similar repositories for FastQC

Users that are interested in FastQC are comparing it to the libraries listed below

• FelixKrueger / TrimGalore
  A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS…
  ☆527Updated last month
• NBISweden / AGAT
  Another Gtf/Gff Analysis Toolkit https://nbisweden.github.io/AGAT/
  ☆535Updated last month
• davidemms / OrthoFinder
  Phylogenetic orthology inference for comparative genomics
  ☆803Updated 3 months ago
• deeptools / deepTools
  Tools to process and analyze deep sequencing data.
  ☆741Updated 3 months ago
• DaehwanKimLab / hisat2
  Graph-based alignment (Hierarchical Graph FM index)
  ☆514Updated last month
• gpertea / stringtie
  Transcript assembly and quantification for RNA-Seq
  ☆470Updated this week
• DerrickWood / kraken2
  The second version of the Kraken taxonomic sequence classification system
  ☆837Updated last week
• nf-core / sarek
  Analysis pipeline to detect germline or somatic variants (pre-processing, variant calling and annotation) from WGS / targeted sequencing
  ☆492Updated this week
• FelixKrueger / Bismark
  A tool to map bisulfite converted sequence reads and determine cytosine methylation states
  ☆434Updated 2 months ago
• eggnogdb / eggnog-mapper
  Fast genome-wide functional annotation through orthology assignment
  ☆664Updated 4 months ago
• mikolmogorov / Flye
  De novo assembler for single molecule sequencing reads using repeat graphs
  ☆878Updated 5 months ago
• deweylab / RSEM
  RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
  ☆454Updated last year
• gpertea / gffread
  GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more
  ☆441Updated 10 months ago
• ablab / spades
  SPAdes Genome Assembler
  ☆871Updated 2 weeks ago
• usadellab / Trimmomatic
  ☆271Updated last week
• macs3-project / MACS
  MACS -- Model-based Analysis of ChIP-Seq
  ☆756Updated last week
• pachterlab / kallisto
  Near-optimal RNA-Seq quantification
  ☆703Updated 6 months ago
• deeptools / pyGenomeTracks
  python module to plot beautiful and highly customizable genome browser tracks
  ☆845Updated last year
• bwa-mem2 / bwa-mem2
  The next version of bwa-mem
  ☆788Updated last week
• dellytools / delly
  DELLY2: Structural variant discovery by integrated paired-end and split-read analysis
  ☆488Updated 2 months ago
• CGATOxford / UMI-tools
  Tools for handling Unique Molecular Identifiers in NGS data sets
  ☆526Updated 3 months ago
• thelovelab / DESeq2
  Differential expression of RNA-seq data using the Negative Binomial
  ☆418Updated last week
• BenLangmead / bowtie2
  A fast and sensitive gapped read aligner
  ☆747Updated last month
• rrwick / Unicycler
  hybrid assembly pipeline for bacterial genomes
  ☆623Updated last year
• tanghaibao / jcvi
  Python library to facilitate genome assembly, annotation, and comparative genomics
  ☆865Updated 2 months ago
• MultiQC / MultiQC
  Aggregate results from bioinformatics analyses across many samples into a single report.
  ☆1,372Updated this week
• fritzsedlazeck / Sniffles
  Structural variation caller using third generation sequencing
  ☆622Updated this week
• chhylp123 / hifiasm
  Hifiasm: a haplotype-resolved assembler for accurate Hifi reads
  ☆686Updated 7 months ago
• jorvis / biocode
  Bioinformatics code libraries and scripts
  ☆546Updated 3 months ago
• bactopia / bactopia
  A flexible pipeline for complete analysis of bacterial genomes
  ☆480Updated this week