Repositories list

• internal

  Public
  0•0•0•0•Updated Feb 7, 2025Feb 7, 2025

• SibeliaZ

  Public
  A fast whole-genome aligner based on de Bruijn graphs

  bioinformaticsgenomicsgraph-algorithms+ 5comparative-genomicsde-bruijn-graphswhole-genome-alignmentlocally-collinear-blocksalignment

  C++

  •

  Other

  •19•142•36•0•Updated Feb 2, 2025Feb 2, 2025

• TwoPaCo

  Public
  A fast constructor of the compressed de Bruijn graph from many genomes

  bioinformaticsgenomicsgraph-algorithms+ 2comparative-genomicsde-bruijn-graphs

  C++

  •

  Other

  •10•40•12•1•Updated Feb 2, 2025Feb 2, 2025

• eskemap

  Public
  Sources for sketch-based all-hits read mapping paper

  C

  •

  GNU General Public License v3.0

  •1•2•0•0•Updated Dec 2, 2024Dec 2, 2024

• pla-index

  Public
  C++

  •

  MIT License

  •0•5•0•0•Updated Jun 21, 2024Jun 21, 2024

• ESSColor

  Public
  C++

  •2•7•3•0•Updated Jun 15, 2024Jun 15, 2024

• HowDeSBT

  Public
  Sequence Bloom Tree, supporting determined/how split filters

  C++

  •

  MIT License

  •4•10•1•0•Updated Apr 19, 2024Apr 19, 2024

• pla-complexity-figures

  Public
  HTML

  •

  MIT License

  •0•0•0•0•Updated Feb 27, 2024Feb 27, 2024

• ESSCompress

  Public
  C++

  •

  Other

  •1•5•1•0•Updated May 4, 2023May 4, 2023

• assembly-artifacts-paper-experiments

  Public
  Python

  •1•0•0•0•Updated May 6, 2022May 6, 2022

• mutation-rate-intervals

  Public
  Support for "statistics of k-mers from a sequence undergoing a simple mutation process without spurious matches"

  Python

  •2•3•2•0•Updated Mar 14, 2022Mar 14, 2022

• minimizer-jaccard-estimator

  Public
  Support for minimizer Jaccard estimator

  Python

  •0•1•0•0•Updated Mar 12, 2022Mar 12, 2022

• MashMap

  Public
  A fast approximate aligner for long DNA sequences

  C++

  •

  Other

  •39•0•0•0•Updated Nov 10, 2021Nov 10, 2021

• directed-unitigs

  Public
  C++

  •

  Other

  •0•0•0•0•Updated Nov 5, 2021Nov 5, 2021

• UST

  Public
  C++

  •

  GNU General Public License v3.0

  •3•25•1•1•Updated Apr 2, 2021Apr 2, 2021

• BubbZ

  Public
  C++

  •

  Other

  •1•15•1•0•Updated Aug 6, 2020Aug 6, 2020

• varmatch

  Public
  robust matching of small variant datasets using flexible scoring schemes

  C++

  •

  Apache License 2.0

  •6•10•3•1•Updated Mar 26, 2020Mar 26, 2020

• vargeno

  Public
  Towards fast and accurate SNP genotyping from whole genome sequencing data for bedside diagnostics.

  bioinformaticsalgorithmscomputational-biology+ 3data-structuresgenotypingsnps

  C++

  •

  MIT License

  •4•20•5•1•Updated Feb 10, 2019Feb 10, 2019

• bloomtree-allsome

  Public
  Sequence Bloom Trees with All/Some split

  C++

  •

  GNU General Public License v3.0

  •14•11•0•0•Updated Oct 30, 2018Oct 30, 2018

• ContigValidator

  Public
  It outputs the alignment of an assembler using simple exact matching and bwa mem

  OpenEdge ABL

  •3•0•0•0•Updated Oct 15, 2018Oct 15, 2018

• vargeno_lite

  Public
  Memory Lite version of VarGeno

  C++

  •0•0•0•0•Updated Aug 13, 2018Aug 13, 2018

• SbtPlayData

  Public
  Very small examples for testing Sequence Bloom Trees and similar data structures

  0•0•0•0•Updated May 17, 2018May 17, 2018

• refpluspipeline

  Public
  Java

  •3•1•0•0•Updated May 25, 2017May 25, 2017

• bioinformatics_submission_guides

  Public
  Bioinformatics Journal Guides

  0•0•0•0•Updated Nov 21, 2016Nov 21, 2016

• cnfind

  Public
  C++

  •2•2•11•0•Updated May 31, 2015May 31, 2015

• isvda

  Public
  iterative small variant detecting algorithm

  Python

  •1•1•0•0•Updated May 23, 2015May 23, 2015

• test

  Public
  This is an empty repository for the purposes of figuring out how github works

  0•0•0•0•Updated Mar 7, 2014Mar 7, 2014