Alternatives and similar repositories for fastp

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

• MultiQC / MultiQC
  Aggregate results from bioinformatics analyses across many samples into a single report.
  ☆1,318Updated 2 weeks ago
• lh3 / seqtk
  Toolkit for processing sequences in FASTA/Q formats
  ☆1,471Updated 3 weeks ago
• lh3 / bwa
  Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
  ☆1,623Updated 3 months ago
• DerrickWood / kraken2
  The second version of the Kraken taxonomic sequence classification system
  ☆801Updated 2 weeks ago
• crazyhottommy / RNA-seq-analysis
  RNAseq analysis notes from Ming Tang
  ☆1,014Updated 3 years ago
• nf-core / rnaseq
  RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
  ☆1,046Updated 2 weeks ago
• macs3-project / MACS
  MACS -- Model-based Analysis of ChIP-Seq
  ☆746Updated 2 months ago
• trinityrnaseq / trinityrnaseq
  Trinity RNA-Seq de novo transcriptome assembly
  ☆860Updated 4 months ago
• tseemann / prokka
  Rapid prokaryotic genome annotation
  ☆906Updated last year
• arq5x / bedtools2
  bedtools - the swiss army knife for genome arithmetic
  ☆981Updated 3 months ago
• samtools / samtools
  Tools (written in C using htslib) for manipulating next-generation sequencing data
  ☆1,739Updated last week
• davidemms / OrthoFinder
  Phylogenetic orthology inference for comparative genomics
  ☆778Updated 8 months ago
• DaehwanKimLab / hisat2
  Graph-based alignment (Hierarchical Graph FM index)
  ☆502Updated 7 months ago
• COMBINE-lab / salmon
  🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
  ☆811Updated last year
• bwa-mem2 / bwa-mem2
  The next version of bwa-mem
  ☆762Updated 10 months ago
• mikolmogorov / Flye
  De novo assembler for single molecule sequencing reads using repeat graphs
  ☆843Updated last month
• eggnogdb / eggnog-mapper
  Fast genome-wide functional annotation through orthology assignment
  ☆625Updated this week
• s-andrews / FastQC
  A quality control analysis tool for high throughput sequencing data
  ☆510Updated last year
• ablab / spades
  SPAdes Genome Assembler
  ☆842Updated last month
• FelixKrueger / TrimGalore
  A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS…
  ☆510Updated 3 months ago
• lh3 / minimap2
  A versatile pairwise aligner for genomic and spliced nucleotide sequences
  ☆1,985Updated last week
• cmdcolin / awesome-genome-visualization
  A list of interesting genome browser and genome visualization programs
  ☆972Updated this week
• crazyhottommy / ChIP-seq-analysis
  ChIP-seq analysis notes from Ming Tang
  ☆805Updated 10 months ago
• tanghaibao / jcvi
  Python library to facilitate genome assembly, annotation, and comparative genomics
  ☆830Updated this week
• BenLangmead / bowtie2
  A fast and sensitive gapped read aligner
  ☆720Updated 6 months ago
• jorvis / biocode
  Bioinformatics code libraries and scripts
  ☆528Updated 4 months ago
• kblin / ncbi-genome-download
  Scripts to download genomes from the NCBI FTP servers
  ☆1,013Updated 10 months ago
• twbattaglia / RNAseq-workflow
  A repository for setting up a RNAseq workflow
  ☆430Updated 8 years ago
• rrwick / Bandage
  a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
  ☆619Updated 2 years ago
• YuLab-SMU / clusterProfiler
  A universal enrichment tool for interpreting omics data
  ☆1,097Updated 2 months ago