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    38 repositories

    • seqrequester

      Public
      A tool for summarizing, extracting, generating and modifying DNA sequences.
      C
      •4•23•2•0•Updated Oct 31, 2024Oct 31, 2024

    • meryl-utility

      Public
      A collection of miscellaneous code used by Meryl, Canu and others.
      C
      •3•1•0•0•Updated Oct 31, 2024Oct 31, 2024

    • T2T-Browser

      Public
      Genome browser hub for the T2T genomes and resources
      HTML
      •3•16•0•0•Updated Oct 31, 2024Oct 31, 2024

    • verkko

      Public
      Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and Oxford Nanopore ultra-long reads.
      Python
      •29•297•23•0•Updated Oct 28, 2024Oct 28, 2024

    • Primates

      Public
      Complete assemblies of non-human primate genomes
      Other
      •3•38•1•0•Updated Oct 14, 2024Oct 14, 2024

    • MashMap

      Public
      A fast approximate aligner for long DNA sequences
      C++
      •
      Other
      •39•267•21•0•Updated Oct 11, 2024Oct 11, 2024

    • ModDotPlot

      Public
      Python
      •
      MIT License
      •9•118•5•0•Updated Oct 6, 2024Oct 6, 2024

    • canu

      Public
      A single molecule sequence assembler for genomes large and small.
      C++
      •179•658•6•2•Updated Sep 30, 2024Sep 30, 2024

    • parsnp

      Public
      Parsnp was designed to align the core genome of hundreds to thousands of bacterial genomes within a few minutes to few hours. Input can be both draft assemblies and finished genomes, and output includes variant (SNP) calls, core genome phylogeny and multi-alignments. Parsnp leverages contextual information provided by multi-alignments surroundin…
      C++
      •
      Other
      •25•128•28•0•Updated Sep 28, 2024Sep 28, 2024

    • training

      Public
      Genome Assembly 102
      Shell
      •1•11•0•0•Updated Sep 26, 2024Sep 26, 2024

    • MetaCarvel

      Public
      MetaCarvel: A scaffolder for metagenomes
      genome-assemblyscaffoldermetagenomes
      C++
      •
      MIT License
      •16•13•2•2•Updated Sep 17, 2024Sep 17, 2024

    • HG002

      Public
      A complete diploid human genome
      5•96•1•0•Updated Sep 10, 2024Sep 10, 2024

    • CHM13

      Public
      The complete sequence of a human genome
      Other
      •99•916•21•0•Updated Aug 23, 2024Aug 23, 2024

    • HG002-issues

      Public
      HG002 human reference genome issue tracking and polishing
      0•10•38•0•Updated Jul 22, 2024Jul 22, 2024

    • merqury

      Public
      k-mer based assembly evaluation
      Shell
      •
      Other
      •19•282•20•0•Updated Jun 28, 2024Jun 28, 2024

    • Winnowmap

      Public
      Long read / genome alignment software
      nanoporepacbiogenome-analysis
      C
      •
      Other
      •23•257•28•1•Updated Jun 13, 2024Jun 13, 2024

    • SALSA

      Public
      SALSA: A tool to scaffold long read assemblies with Hi-C data
      long-readhicassemblyscaffold
      Python
      •
      MIT License
      •47•180•23•2•Updated May 17, 2024May 17, 2024

    • meryl

      Public
      A genomic k-mer counter (and sequence utility) with nice features.
      C
      •13•114•35•0•Updated May 16, 2024May 16, 2024

    • rukki

      Public
      Extracting paths from assembly graphs
      Rust
      •0•22•18•0•Updated Apr 26, 2024Apr 26, 2024

    • canu-regression

      Public
      Regression test cases and results for Canu.
      Shell
      •0•0•0•0•Updated Apr 5, 2024Apr 5, 2024

    • verkko-regression

      Public
      Test suite for Verkko.
      Perl
      •0•0•0•0•Updated Jan 25, 2024Jan 25, 2024

    • CHM13-issues

      Public
      CHM13 human reference genome issue tracking
      HTML
      •
      Other
      •3•18•0•0•Updated Jan 18, 2024Jan 18, 2024

    • MetagenomeScope

      Public
      Visualization tool for (meta)genome assembly graphs
      bioinformaticsmetagenomicsgenome-assemblyvisualization
      JavaScript
      •
      GNU General Public License v3.0
      •8•24•124•1•Updated Jan 3, 2024Jan 3, 2024

    • harvest-tools

      Public
      C++
      •
      Other
      •6•8•15•0•Updated Dec 19, 2023Dec 19, 2023

    • gingr

      Public
      C++
      •
      Other
      •5•13•15•1•Updated Dec 5, 2023Dec 5, 2023

    • Mash

      Public
      Fast genome and metagenome distance estimation using MinHash
      C++
      •
      Other
      •91•389•80•3•Updated Oct 26, 2023Oct 26, 2023

    • MHAP

      Public
      MinHash Alignment Process (MHAP, pronounced MAP): locality-sensitive hashing to detect long-read overlaps and utilities
      Java
      •
      Apache License 2.0
      •13•96•0•0•Updated Jun 27, 2022Jun 27, 2022

    • MUMmer3

      Public
      MUMmer3
      C++
      •
      Other
      •9•15•8•2•Updated Jan 12, 2022Jan 12, 2022

    • Krona

      Public
      Interactively explore metagenomes and more from a web browser.
      JavaScript
      •102•464•117•2•Updated Dec 22, 2021Dec 22, 2021

    • binnacle

      Public
      Binnacle: Using Scaffolds to Improve the Contiguity and Quality of Metagenomic Bins
      metagenomicsbinningscaffoldingmetagenome-assemblymetagenome-assembled-genomeschangepoint-detection
      Python
      •2•11•0•0•Updated Dec 7, 2021Dec 7, 2021