Alternatives and similar repositories for needle

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

• edawson / mkmh
  Generate kmers/minimizers/hashes/MinHash signatures, including with multiple kmer sizes.
  ☆24Updated 4 years ago
• bioinfologics / sdg
  Sequence Distance Graph framework: graph + reads + mapping + analysis
  ☆25Updated 3 years ago
• edawson / svaha
  Convert structural variants to sequence graphs [ VCF + FASTA ---> GFA ]
  ☆12Updated last year
• iqbal-lab / cortex
  reference free variant assembly
  ☆33Updated last year
• prophyle / prophasm
  ProphAsm – a rapid computation of simplitigs directly from k-mer sets
  ☆26Updated 2 years ago
• shenwei356 / strobemers
  A Go implementation of the strobemers (https://github.com/ksahlin/strobemers)
  ☆15Updated 4 years ago
• karel-brinda / ococo
  Ococo: the first online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream.
  ☆47Updated 6 years ago
• nanoporetech / minimappy
  Python bindings to minimap2
  ☆16Updated 7 years ago
• richarddurbin / modimizer
  a toolset for fast DNA read set matching and assembly using a new type of reduced kmer
  ☆37Updated 3 years ago
• rvaser / rala
  Layout module for raw de novo genome assembly of long uncorrected reads.
  ☆21Updated 4 years ago
• edawson / svaha2
  Linear-time, low-memory construction of variation graphs
  ☆20Updated 5 years ago
• lh3 / rmaxcut
  An experimental tool to find approximate max-cuts in a large graph
  ☆11Updated 4 years ago
• edawson / rkmh
  Classify sequencing reads using MinHash.
  ☆48Updated 5 years ago
• lh3 / gfa1
  This repo is deprecated. Please use gfatools instead.
  ☆16Updated 6 years ago
• vgteam / gssw
  efficient alignment of strings to partially ordered string graphs
  ☆33Updated 3 years ago
• lh3 / pre-pe
  Preprocessing paired-end reads produced with experiment-specific protocols
  ☆32Updated 7 years ago
• ocxtal / rbread
  Header-only, gzread-like reader for gzip, bz2, and xz.
  ☆12Updated 6 years ago
• SJTU-CGM / CDKAM
  ☆10Updated 4 years ago
• jltsiren / gbwtgraph
  GBWT-based handle graph
  ☆31Updated 3 months ago
• wang-q / intspan
  Command line tools for IntSpan related bioinformatics operations
  ☆13Updated 2 months ago
• annalam / seqkit
  Toolkit for manipulating FASTA and SAM files
  ☆18Updated last year
• rvaser / bioparser
  C++ library for parsing several formats in bioinformatics
  ☆9Updated 2 years ago
• gregorykucherov / spaced-seeds-for-metagenomics
  ☆14Updated 9 years ago
• mklarqvist / libflagstats
  Efficient C functions to compute the summary statistics (flagstats) for sequencing read sets.
  ☆15Updated 5 years ago
• jaudoux / kamix
  Index and query k-mer matrices in BGZF
  ☆12Updated 7 years ago
• VGP / vgp-tools
  ☆28Updated 2 months ago
• natir / fpa
  Filter of Pairwise Alignement
  ☆44Updated 3 years ago
• NCBI-Codeathons / SWIGG
  A pipeline for making SWIft Genomes in a Graph (SWIGG) using k-mers
  ☆22Updated 5 years ago
• csiro-crop-informatics / biokanga
  An integrated high performance bioinformatics toolkit
  ☆23Updated 6 years ago
• yhoogstrate / fastafs
  toolkit for file system virtualisation of random access compressed FASTA, FAI, DICT & TWOBIT files
  ☆22Updated 10 months ago