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    44 repositories

    • MetagenomeScope

      Public
      Visualization tool for (meta)genome assembly graphs
      visualizationbioinformaticsmetagenomics
      visualizationbioinformaticsmetagenomicsgenome-assembly
      Python
      •
      GNU General Public License v3.0
      •9•46•139•0•Updated Apr 18, 2026Apr 18, 2026

    • gingr

      Public
      C++
      •
      Other
      •6•14•15•1•Updated Apr 15, 2026Apr 15, 2026

    • MetaCompass

      Public
      MetaCompass: Reference-guided Assembly of Metagenomes
      Python
      •
      Other
      •12•43•12•0•Updated Apr 13, 2026Apr 13, 2026

    • MetaCarvel

      Public
      MetaCarvel: A scaffolder for metagenomes
      scaffoldermetagenomesgenome-assembly
      scaffoldermetagenomesgenome-assembly
      C++
      •
      MIT License
      •17•14•3•3•Updated Apr 13, 2026Apr 13, 2026

    • verkko

      Public
      Telomere-to-telomere assembly of accurate long reads (PacBio HiFi, Oxford Nanopore Duplex, HERRO corrected Oxford Nanopore Simplex) and Oxford Nanopore ultra-lo…
      Python
      •34•388•18•0•Updated Apr 10, 2026Apr 10, 2026

    • verkko-fillet

      Public
      Post-verkko graph and assembly curation in Python.
      Jupyter Notebook
      •
      MIT License
      •0•18•5•0•Updated Apr 9, 2026Apr 9, 2026

    • KOLF2.1J-Diploid-Assembly

      Public
      The personalized diploid genome of KOLF iPSC cell line
      0•0•2•0•Updated Apr 7, 2026Apr 7, 2026

    • TTT

      Public
      Python
      •0•14•3•0•Updated Apr 7, 2026Apr 7, 2026

    • T2T-Browser

      Public
      Genome browser hub for the T2T genomes and resources
      HTML
      •3•27•0•0•Updated Apr 7, 2026Apr 7, 2026

    • GQC

      Public
      Python package for comparing genome assemblies and read data to the diploid Q100 benchmark
      Python
      •
      Other
      •1•15•2•0•Updated Mar 31, 2026Mar 31, 2026

    • HG002

      Public
      A complete diploid human genome
      5•145•2•0•Updated Mar 27, 2026Mar 27, 2026

    • DJCounter

      Public
      This repository can be used to calculate the number of DJ counts in the genome aligned to the GRCh38 (broad reference).
      Jupyter Notebook
      •0•3•0•0•Updated Mar 10, 2026Mar 10, 2026

    • anianns

      Public
      ANI based satellite annotation
      Python
      •0•26•1•0•Updated Mar 2, 2026Mar 2, 2026

    • canu

      Public
      A single molecule sequence assembler for genomes large and small.
      C++
      •180•700•6•2•Updated Feb 24, 2026Feb 24, 2026

    • ModDotPlot

      Public
      Python
      •
      MIT License
      •11•188•6•0•Updated Feb 10, 2026Feb 10, 2026

    • meryl-utility

      Public
      A collection of miscellaneous code used by Meryl, Canu and others.
      C
      •3•1•0•0•Updated Dec 16, 2025Dec 16, 2025

    • Winnowmap

      Public
      Long read / genome alignment software
      nanoporepacbiogenome-analysis
      nanoporepacbiogenome-analysis
      C
      •
      Other
      •31•315•33•1•Updated Dec 16, 2025Dec 16, 2025

    • 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…
      C++
      •
      Other
      •27•154•30•0•Updated Oct 2, 2025Oct 2, 2025

    • Mash

      Public
      Fast genome and metagenome distance estimation using MinHash
      C++
      •
      Other
      •94•440•85•3•Updated Sep 19, 2025Sep 19, 2025

    • HG002-issues

      Public
      HG002 human reference genome issue tracking and polishing
      0•11•30•0•Updated Sep 11, 2025Sep 11, 2025

    • CHM13

      Public
      The complete sequence of a human genome
      Other
      •101•1k•27•0•Updated Jul 14, 2025Jul 14, 2025

    • meryl

      Public
      A genomic k-mer counter (and sequence utility) with nice features.
      C
      •15•165•38•0•Updated Jul 4, 2025Jul 4, 2025

    • Primates

      Public
      Complete assemblies of non-human primate genomes
      Other
      •4•59•1•0•Updated May 20, 2025May 20, 2025

    • training

      Public
      Genome Assembly 102
      Shell
      •3•18•0•0•Updated Apr 23, 2025Apr 23, 2025

    • seqrequester

      Public
      A tool for summarizing, extracting, generating and modifying DNA sequences.
      C
      •4•23•2•0•Updated Dec 17, 2024Dec 17, 2024

    • harvest-tools

      Public
      C++
      •
      Other
      •6•10•19•0•Updated Dec 16, 2024Dec 16, 2024

    • MashMap

      Public
      A fast approximate aligner for long DNA sequences
      C++
      •
      Other
      •38•287•23•0•Updated Oct 11, 2024Oct 11, 2024

    • merqury

      Public
      k-mer based assembly evaluation
      Shell
      •
      Other
      •25•342•41•2•Updated Jun 28, 2024Jun 28, 2024

    • SALSA

      Public
      SALSA: A tool to scaffold long read assemblies with Hi-C data
      assemblyscaffoldlong-read
      assemblyscaffoldlong-readhic
      Python
      •
      MIT License
      •48•189•23•2•Updated May 17, 2024May 17, 2024

    • rukki

      Public
      Extracting paths from assembly graphs
      Rust
      •0•24•19•0•Updated Apr 26, 2024Apr 26, 2024
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