Alternatives and similar repositories for squeakr

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

• ekg / fastahack
  utilities for indexing and sequence extraction from FASTA files
  ☆59Updated 4 years ago
• cosmo-team / cosmo
  Cosmo is a fast, low-memory DNA assembler using a Succinct (variable order) de Bruijn Graph.
  ☆51Updated last year
• jltsiren / gbwt
  Substring index for paths in a graph
  ☆60Updated last month
• bcgsc / LINKS
  ⛓ Long Interval Nucleotide K-mer Scaffolder
  ☆74Updated 2 months ago
• pmelsted / KmerStream
  Streaming algorithm for computing kmer statistics for massive genomics datasets
  ☆54Updated 5 years ago
• ksahlin / strobemers
  A repository for generating strobemers and evalaution
  ☆78Updated last year
• rrwick / Minipolish
  A tool for Racon polishing of miniasm assemblies
  ☆75Updated 4 years ago
• bcgsc / ntCard
  Estimating k-mer coverage histogram of genomics data
  ☆78Updated last year
• arq5x / grabix
  a wee tool for random access into BGZF files.
  ☆84Updated 7 years ago
• tk2 / RetroSeq
  RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference…
  ☆66Updated 2 years ago
• lh3 / fermi-lite
  Standalone C library for assembling Illumina short reads in small regions
  ☆72Updated 2 years ago
• bcgsc / biobloom
  Create Bloom filters for a given reference and then use it to categorize sequences
  ☆76Updated 6 months ago
• edawson / gfakluge
  A C++ library and utilities for manipulating the Graphical Fragment Assembly format.
  ☆54Updated 3 years ago
• kamimrcht / REINDEER
  REINDEER REad Index for abuNDancE quERy
  ☆58Updated 10 months ago
• bcgsc / arcs
  🌈Scaffold genome sequence assemblies using linked or long read sequencing data
  ☆94Updated 6 months ago
• will-rowe / hulk
  Histosketching Using Little Kmers
  ☆57Updated 2 years ago
• COMBINE-lab / pufferfish
  An efficient index for the colored, compacted, de Bruijn graph
  ☆110Updated 7 months ago
• benedictpaten / sonLib
  Small general purpose library for C and Python with focus on bioinformatics.
  ☆30Updated 2 years ago
• lbcb-sci / graphmap2
  GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/n…
  ☆67Updated 2 years ago
• conchoecia / pauvre
  Pauvre: QC and genome browser plotting Oxford Nanopore and PacBio long reads.
  ☆54Updated 6 months ago
• ekg / seqwish
  alignment to variation graph inducer
  ☆148Updated 3 months ago
• mcveanlab / mccortex
  De novo genome assembly and multisample variant calling
  ☆112Updated 6 years ago
• sestaton / Transposome
  A toolkit for annotation of transposable element families from unassembled sequence reads
  ☆30Updated 2 years ago
• natir / yacrd
  Yet Another Chimeric Read Detector
  ☆80Updated 6 months ago
• thegenemyers / DALIGNER
  Find all significant local alignments between reads
  ☆141Updated 11 months ago
• ydLiu-HIT / deSALT
  deSALT - De Bruijn graph-based Spliced Aligner for Long Transcriptome reads
  ☆44Updated 2 years ago
• mateidavid / fast5
  A C++ header-only library for reading Oxford Nanopore Fast5 files
  ☆53Updated 2 years ago
• lh3 / sdust
  Symmetric DUST for finding low-complexity regions in DNA sequences
  ☆42Updated last year
• bioinformatics-centre / BayesTyper
  A method for variant graph genotyping based on exact alignment of k-mers
  ☆86Updated 6 years ago
• mateidavid / nanocall
  An Oxford Nanopore Basecaller
  ☆71Updated 3 years ago