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.
  ☆1,337Updated this week
• lh3 / seqtk
  Toolkit for processing sequences in FASTA/Q formats
  ☆1,480Updated 2 months ago
• nf-core / rnaseq
  RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
  ☆1,076Updated last week
• trinityrnaseq / trinityrnaseq
  Trinity RNA-Seq de novo transcriptome assembly
  ☆866Updated 5 months ago
• jorvis / biocode
  Bioinformatics code libraries and scripts
  ☆536Updated 2 weeks ago
• ncbi / sra-tools
  SRA Tools
  ☆1,245Updated this week
• crazyhottommy / RNA-seq-analysis
  RNAseq analysis notes from Ming Tang
  ☆1,019Updated 3 years ago
• davidemms / OrthoFinder
  Phylogenetic orthology inference for comparative genomics
  ☆786Updated 3 weeks ago
• s-andrews / FastQC
  A quality control analysis tool for high throughput sequencing data
  ☆520Updated last year
• tanghaibao / jcvi
  Python library to facilitate genome assembly, annotation, and comparative genomics
  ☆838Updated last week
• cmdcolin / awesome-genome-visualization
  A list of interesting genome browser and genome visualization programs
  ☆987Updated last week
• kblin / ncbi-genome-download
  Scripts to download genomes from the NCBI FTP servers
  ☆1,023Updated last week
• lh3 / bwa
  Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)
  ☆1,636Updated 4 months ago
• bwa-mem2 / bwa-mem2
  The next version of bwa-mem
  ☆771Updated last month
• BenLangmead / bowtie2
  A fast and sensitive gapped read aligner
  ☆727Updated 7 months ago
• COMBINE-lab / salmon
  🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using selective alignment
  ☆814Updated last year
• macs3-project / MACS
  MACS -- Model-based Analysis of ChIP-Seq
  ☆751Updated last week
• lh3 / minimap2
  A versatile pairwise aligner for genomic and spliced nucleotide sequences
  ☆2,005Updated last month
• crazyhottommy / ChIP-seq-analysis
  ChIP-seq analysis notes from Ming Tang
  ☆812Updated last year
• shenwei356 / seqkit
  A cross-platform and ultrafast toolkit for FASTA/Q file manipulation
  ☆1,446Updated 3 weeks ago
• arq5x / bedtools2
  bedtools - the swiss army knife for genome arithmetic
  ☆988Updated 4 months ago
• ablab / spades
  SPAdes Genome Assembler
  ☆853Updated this week
• griffithlab / rnaseq_tutorial
  Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis inclu…
  ☆1,379Updated 2 years ago
• DerrickWood / kraken2
  The second version of the Kraken taxonomic sequence classification system
  ☆811Updated last week
• samtools / samtools
  Tools (written in C using htslib) for manipulating next-generation sequencing data
  ☆1,753Updated 2 weeks ago
• deeptools / deepTools
  Tools to process and analyze deep sequencing data.
  ☆726Updated 2 weeks ago
• DaehwanKimLab / hisat2
  Graph-based alignment (Hierarchical Graph FM index)
  ☆507Updated 8 months ago
• tseemann / prokka
  Rapid prokaryotic genome annotation
  ☆919Updated last year
• FelixKrueger / TrimGalore
  A wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS…
  ☆519Updated 4 months ago
• eggnogdb / eggnog-mapper
  Fast genome-wide functional annotation through orthology assignment
  ☆640Updated last month