Alternatives and similar repositories for fastq-tools

Users that are interested in fastq-tools are comparing it to the libraries listed below

• jstjohn / SeqPrep
  Tool for stripping adaptors and/or merging paired reads with overlap into single reads.
  ☆145Updated 9 years ago
• alastair-droop / fqtools
  An efficient FASTQ manipulation suite
  ☆138Updated 6 years ago
• andyrimmer / Platypus
  Platypus Variant Caller
  ☆108Updated last year
• nh13 / DWGSIM
  Whole Genome Simulator for Next-Generation Sequencing
  ☆102Updated last month
• MikkelSchubert / adapterremoval
  AdapterRemoval v2 - rapid adapter trimming, identification, and read merging
  ☆114Updated last week
• genome-in-a-bottle / giab_latest_release
  This repository contains information about latest release from Genome in a Bottle project
  ☆75Updated 6 years ago
• mozack / abra2
  ABRA2
  ☆95Updated 3 years ago
• statgen / bamUtil
  ☆92Updated 4 years ago
• dnanexus-rnd / GLnexus
  Scalable gVCF merging and joint variant calling for population sequencing projects
  ☆174Updated last year
• genome / breakdancer
  SV detection from paired end reads mapping
  ☆118Updated 6 years ago
• GregoryFaust / samblaster
  samblaster: a tool to mark duplicates and extract discordant and split reads from sam files.
  ☆238Updated 4 years ago
• walaj / SeqLib
  C++ htslib/bwa-mem/fermi interface for interrogating sequence data
  ☆138Updated 4 months ago
• parklab / bamsnap
  ☆122Updated 6 months ago
• CCDG / Pipeline-Standardization
  ☆81Updated 7 years ago
• lh3 / fermikit
  De novo assembly based variant calling pipeline for Illumina short reads
  ☆110Updated 5 years ago
• PacificBiosciences / DevNet
  The DevNet project on github stores the PacBio DevNet website.
  ☆115Updated 7 years ago
• hall-lab / svtyper
  Bayesian genotyper for structural variants
  ☆136Updated 4 years ago
• jdidion / atropos
  An NGS read trimming tool that is specific, sensitive, and speedy. (production)
  ☆126Updated 9 months ago
• dnanexus-archive / parliament2
  Runs a combination of tools to generate structural variant calls on whole-genome sequencing data
  ☆103Updated 5 years ago
• JohnLonginotto / pybam
  Very simple, pure python, BAM file reader
  ☆79Updated 6 years ago
• COMBINE-lab / RapMap
  Rapid sensitive and accurate read mapping via quasi-mapping
  ☆90Updated 5 years ago
• brentp / jigv
  igv.js standalone page generator and automatic configuration to view bam/cram/vcf/bed. "working in under 1 minute"
  ☆131Updated 3 months ago
• zstephens / neat-genreads
  NEAT read simulation tools
  ☆101Updated 3 years ago
• tobiasrausch / alfred
  BAM Statistics, Feature Counting and Annotation
  ☆152Updated this week
• Griffan / VerifyBamID
  VerifyBamID2: A robust tool for DNA contamination estimation from sequence reads using ancestry-agnostic method.
  ☆99Updated last year
• Illumina / Pisces
  Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows.
  ☆99Updated 3 years ago
• walaj / svaba
  Structural variation and indel detection by local assembly
  ☆251Updated 4 months ago
• Oshlack / Corset
  Software for clustering de novo assembled transcripts and counting overlapping reads
  ☆76Updated 4 years ago
• lh3 / bedtk
  A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)
  ☆143Updated 5 months ago
• AndersenLab / VCF-kit
  VCF-kit: Assorted utilities for the variant call format
  ☆132Updated 7 months ago