Alternatives and similar repositories for readfq

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

• MikkelSchubert / adapterremoval
  AdapterRemoval v2 - rapid adapter trimming, identification, and read merging
  ☆113Updated 2 months ago
• alimanfoo / pysamstats
  A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM …
  ☆195Updated last week
• jstjohn / SeqPrep
  Tool for stripping adaptors and/or merging paired reads with overlap into single reads.
  ☆144Updated 8 years ago
• rrwick / Deepbinner
  a signal-level demultiplexer for Oxford Nanopore reads
  ☆126Updated 4 years ago
• linsalrob / fastq-pair
  Match up paired end fastq files quickly and efficiently.
  ☆151Updated last year
• lh3 / gfatools
  Tools for manipulating sequence graphs in the GFA and rGFA formats
  ☆234Updated 11 months ago
• parklab / bamsnap
  ☆123Updated last week
• rrwick / Long-read-assembler-comparison
  Benchmarking of long-read assembly tools for bacterial whole genomes
  ☆171Updated 4 years ago
• alastair-droop / fqtools
  An efficient FASTQ manipulation suite
  ☆138Updated 5 years ago
• sunbeam-labs / sunbeam
  A robust, extensible metagenomics pipeline
  ☆172Updated this week
• adamewing / methylartist
  Tools for plotting methylation data in various ways
  ☆159Updated this week
• tseemann / any2fasta
  Convert various sequence formats to FASTA
  ☆138Updated 3 years ago
• ComparativeGenomicsToolkit / hal
  Hierarchical Alignment Format
  ☆170Updated 7 months ago
• timkahlke / LongRead_tutorials
  Workflows and tutorials for LongRead analysis with specific focus on Oxford Nanopore data
  ☆141Updated 2 weeks ago
• biocorecrg / master_of_pores
  Nextflow pipeline for analysis of direct RNA Nanopore reads
  ☆106Updated last month
• PacificBiosciences / DevNet
  The DevNet project on github stores the PacBio DevNet website.
  ☆116Updated 7 years ago
• nanoporetech / pychopper
  A tool to identify, orient, trim and rescue full length cDNA reads
  ☆82Updated 3 years ago
• fhcrc / seqmagick
  An imagemagick-like frontend to Biopython SeqIO
  ☆115Updated last year
• CSB5 / lofreq
  LoFreq Star: Sensitive variant calling from sequencing data
  ☆105Updated 3 years ago
• giesselmann / nanopype
  Snakemake pipelines for nanopore sequencing data archiving and processing
  ☆91Updated 3 years ago
• ksahlin / strobealign
  Aligns short reads using dynamic seed size with strobemers
  ☆175Updated this week
• fbreitwieser / krakenuniq
  🐙 KrakenUniq: Metagenomics classifier with unique k-mer counting for more specific results
  ☆235Updated last year
• OpenGene / fastv
  An ultra-fast tool for identification of SARS-CoV-2 and other microbes from sequencing data. This tool can be used to detect viral infect…
  ☆118Updated last year
• malonge / RaGOO
  RaGOO is no longer supported. Please use RagTag instead: https://github.com/malonge/RagTag
  ☆172Updated 4 years ago
• roblanf / minion_qc
  Quality control for MinION sequencing data
  ☆217Updated 2 years ago
• NAL-i5K / GFF3toolkit
  Python programs for processing GFF3 files
  ☆98Updated last year
• nh13 / DWGSIM
  Whole Genome Simulator for Next-Generation Sequencing
  ☆99Updated 8 months ago
• HadrienG / InSilicoSeq
  A sequencing simulator
  ☆203Updated last month
• rrwick / Badread
  a long read simulator that can imitate many types of read problems
  ☆241Updated last year
• PacificBiosciences / pbsv
  pbsv - PacBio structural variant (SV) calling and analysis tools
  ☆155Updated 5 months ago