splatlab / squeakr

Related projects ⓘ

Alternatives and complementary repositories for squeakr

• ekg / fastahack
  utilities for indexing and sequence extraction from FASTA files
  ☆59Updated 3 years ago
• bcgsc / ntCard
  Estimating k-mer coverage histogram of genomics data
  ☆76Updated 11 months ago
• bioinformatics-centre / BayesTyper
  A method for variant graph genotyping based on exact alignment of k-mers
  ☆87Updated 5 years ago
• cosmo-team / cosmo
  Cosmo is a fast, low-memory DNA assembler using a Succinct (variable order) de Bruijn Graph.
  ☆51Updated 8 months ago
• lh3 / fermi-lite
  Standalone C library for assembling Illumina short reads in small regions
  ☆72Updated last year
• COMBINE-lab / pufferfish
  An efficient index for the colored, compacted, de Bruijn graph
  ☆108Updated last month
• mcveanlab / mccortex
  De novo genome assembly and multisample variant calling
  ☆113Updated 5 years ago
• will-rowe / hulk
  Histosketching Using Little Kmers
  ☆55Updated last year
• karel-brinda / ococo
  Ococo: the first online variant and consensus caller. Call genomic consensus directly from an unsorted SAM/BAM stream.
  ☆47Updated 5 years ago
• natir / yacrd
  Yet Another Chimeric Read Detector
  ☆72Updated 2 weeks ago
• glennhickey / progressiveCactus
  Distribution package for the Prgressive Cactus multiple genome aligner. Dependencies are linked as submodules
  ☆83Updated 6 years ago
• thegenemyers / DALIGNER
  Find all significant local alignments between reads
  ☆139Updated 4 months ago
• rrwick / Minipolish
  A tool for Racon polishing of miniasm assemblies
  ☆73Updated 3 years ago
• mklarqvist / tomahawk
  Fast calculations of linkage-disequilibrium in large-scale human cohorts
  ☆41Updated 5 years ago
• bcgsc / LINKS
  ⛓ Long Interval Nucleotide K-mer Scaffolder
  ☆73Updated 11 months ago
• ydLiu-HIT / deSALT
  deSALT - De Bruijn graph-based Spliced Aligner for Long Transcriptome reads
  ☆44Updated 2 years ago
• lh3 / unimap
  A EXPERIMENTAL fork of minimap2 optimized for assembly-to-reference alignment
  ☆88Updated 3 years ago
• ksahlin / strobemers
  A repository for generating strobemers and evalaution
  ☆77Updated 7 months ago
• bcgsc / arcs
  🌈Scaffold genome sequence assemblies using linked or long read sequencing data
  ☆92Updated 2 weeks ago
• kamimrcht / REINDEER
  REINDEER REad Index for abuNDancE quERy
  ☆57Updated 3 months 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
• jltsiren / gbwt
  Substring index for paths in a graph
  ☆60Updated 2 weeks ago
• sestaton / Transposome
  A toolkit for annotation of transposable element families from unassembled sequence reads
  ☆31Updated last year
• pmelsted / KmerStream
  Streaming algorithm for computing kmer statistics for massive genomics datasets
  ☆53Updated 4 years ago
• conchoecia / pauvre
  Pauvre: QC and genome browser plotting Oxford Nanopore and PacBio long reads.
  ☆52Updated last week
• dzerbino / oases
  De novo transcriptome assembler for short reads
  ☆62Updated 6 years ago
• iqbal-lab-org / gramtools
  Genome inference from a population reference graph
  ☆93Updated 2 years ago
• phasegenomics / FALCON-Phase
  FALCON-Phase integrates PacBio long-read assemblies with Phase Genomics Hi-C data to create phased, diploid, chromosome-scale scaffolds
  ☆74Updated 4 years ago
• arq5x / grabix
  a wee tool for random access into BGZF files.
  ☆84Updated 6 years ago
• VGP / vgp-tools
  ☆28Updated last year