Alternatives and similar repositories for fastq-tools:

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

• nh13 / DWGSIM
  Whole Genome Simulator for Next-Generation Sequencing
  ☆96Updated 4 months ago
• jstjohn / SeqPrep
  Tool for stripping adaptors and/or merging paired reads with overlap into single reads.
  ☆143Updated 8 years ago
• mozack / abra2
  ABRA2
  ☆92Updated 2 years ago
• parklab / bamsnap
  ☆120Updated 5 months ago
• Cibiv / NextGenMap
  NextGenMap is a flexible highly sensitive short read mapping tool that handles much higher mismatch rates than comparable algorithms whil…
  ☆87Updated 5 years ago
• genome-in-a-bottle / giab_latest_release
  This repository contains information about latest release from Genome in a Bottle project
  ☆74Updated 5 years ago
• genome / breakdancer
  SV detection from paired end reads mapping
  ☆117Updated 5 years ago
• walaj / svaba
  Structural variation and indel detection by local assembly
  ☆244Updated last month
• alimanfoo / pysamstats
  A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM …
  ☆194Updated 3 weeks ago
• zstephens / neat-genreads
  NEAT read simulation tools
  ☆98Updated 2 years ago
• alastair-droop / fqtools
  An efficient FASTQ manipulation suite
  ☆137Updated 5 years ago
• mroosmalen / nanosv
  SV caller for nanopore data
  ☆91Updated 4 years ago
• thegenemyers / DALIGNER
  Find all significant local alignments between reads
  ☆141Updated 9 months ago
• JohnLonginotto / pybam
  Very simple, pure python, BAM file reader
  ☆79Updated 6 years ago
• lh3 / minimap
  This repo is DEPRECATED. Please use minimap2, the successor of minimap.
  ☆105Updated 7 years ago
• andyrimmer / Platypus
  Platypus Variant Caller
  ☆108Updated 9 months ago
• BoevaLab / FREEC
  Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
  ☆159Updated 8 months ago
• lh3 / bedtk
  A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)
  ☆140Updated last week
• PacificBiosciences / DevNet
  The DevNet project on github stores the PacBio DevNet website.
  ☆116Updated 6 years ago
• NAL-i5K / GFF3toolkit
  Python programs for processing GFF3 files
  ☆95Updated last year
• nanoporetech / pipeline-structural-variation
  Pipeline for calling structural variations in whole genomes sequencing Oxford Nanopore data
  ☆114Updated 3 years ago
• Oshlack / Corset
  Software for clustering de novo assembled transcripts and counting overlapping reads
  ☆71Updated 3 years ago
• wurmlab / flo
  Same species annotation lift over pipeline.
  ☆97Updated last year
• marbl / HG002
  A complete diploid human genome
  ☆117Updated 3 months ago
• PacificBiosciences / pbsv
  pbsv - PacBio structural variant (SV) calling and analysis tools
  ☆144Updated last month
• ExpressionAnalysis / ea-utils
  Automatically exported from code.google.com/p/ea-utils
  ☆96Updated last year
• COMBINE-lab / RapMap
  Rapid sensitive and accurate read mapping via quasi-mapping
  ☆89Updated 4 years ago
• mkirsche / Jasmine
  Jasmine: SV Merging Across Samples
  ☆210Updated 4 months ago
• walaj / SeqLib
  C++ htslib/bwa-mem/fermi interface for interrogating sequence data
  ☆137Updated 8 months ago
• AndersenLab / VCF-kit
  VCF-kit: Assorted utilities for the variant call format
  ☆129Updated 2 months ago