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    46 repositories

    • MetagenomeScope

      Public
      Visualization tool for (meta)genome assembly graphs
      visualizationbioinformaticsmetagenomics
      visualizationbioinformaticsmetagenomicsgenome-assembly
      Python
      •
      GNU General Public License v3.0
      •10•50•165•0•Updated Sep 10, 2026Sep 10, 2026

    • canu

      Public
      A single molecule sequence assembler for genomes large and small.
      C++
      •178•709•3•2•Updated Sep 10, 2026Sep 10, 2026

    • GQC

      Public
      Python package for comparing genome assemblies and read data to the diploid Q100 benchmark
      Python
      •
      Other
      •3•19•1•0•Updated Sep 3, 2026Sep 3, 2026

    • 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
      •29•157•31•0•Updated Sep 2, 2026Sep 2, 2026

    • harvest-tools

      Public
      C++
      •
      Other
      •7•10•19•0•Updated Sep 2, 2026Sep 2, 2026

    • gis-bulk-assembly

      Public
      Utility scripts to download/process/assemble/qc large collection of samples from AWS/FTP
      Perl
      •0•1•0•0•Updated Sep 1, 2026Sep 1, 2026

    • Pooch

      Public
      POOCH is a Snakemake-based pipeline for assigning chromosome labels and determining the parent of origin (maternal or paternal) of near-complete genome assembli…
      genome-annotationgenome-assembly
      genome-annotationgenome-assembly
      MIT License
      •0•0•0•0•Updated Aug 28, 2026Aug 28, 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•417•19•0•Updated Aug 25, 2026Aug 25, 2026

    • verkko-fillet

      Public
      Post-verkko graph and assembly curation in Python.
      Jupyter Notebook
      •
      MIT License
      •1•33•6•0•Updated Aug 20, 2026Aug 20, 2026

    • MetaCompass

      Public
      MetaCompass: Reference-guided Assembly of Metagenomes
      Python
      •
      Other
      •12•45•13•0•Updated Aug 19, 2026Aug 19, 2026

    • TTT

      Public
      Python
      •0•28•3•0•Updated Aug 18, 2026Aug 18, 2026

    • HG002

      Public
      A complete diploid human genome
      5•159•2•0•Updated Aug 10, 2026Aug 10, 2026

    • T2T-Browser

      Public
      Genome browser hub for the T2T genomes and resources
      HTML
      •3•31•0•0•Updated Aug 10, 2026Aug 10, 2026

    • anianns

      Public
      ANI based satellite annotation
      Python
      •
      MIT License
      •0•29•1•0•Updated Aug 6, 2026Aug 6, 2026

    • HG002-issues

      Public
      HG002 human reference genome issue tracking and polishing
      0•11•31•0•Updated Aug 5, 2026Aug 5, 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
      •
      Other
      •0•6•0•0•Updated Jul 30, 2026Jul 30, 2026

    • meryl

      Public
      A genomic k-mer counter (and sequence utility) with nice features.
      C
      •16•189•37•0•Updated Jul 21, 2026Jul 21, 2026

    • meryl-utility

      Public
      A collection of miscellaneous code used by Meryl, Canu and others.
      C
      •4•1•0•0•Updated Jul 15, 2026Jul 15, 2026

    • merqury

      Public
      k-mer based assembly evaluation
      Shell
      •
      Other
      •25•354•43•2•Updated Jul 6, 2026Jul 6, 2026

    • CHM13

      Public
      The complete sequence of a human genome
      Other
      •104•1.1k•27•0•Updated Jul 3, 2026Jul 3, 2026

    • KOLF2.1J-Diploid-Assembly

      Public
      The personalized diploid genome of KOLF iPSC cell line
      MIT License
      •0•0•1•0•Updated Jun 25, 2026Jun 25, 2026

    • rukki

      Public
      Extracting paths from assembly graphs
      Rust
      •0•26•19•0•Updated Jun 22, 2026Jun 22, 2026

    • gingr

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

    • ModDotPlot

      Public
      Python
      •
      MIT License
      •10•198•7•0•Updated Feb 10, 2026Feb 10, 2026

    • Winnowmap

      Public
      Long read / genome alignment software
      nanoporepacbiogenome-analysis
      nanoporepacbiogenome-analysis
      C
      •
      Other
      •31•331•36•1•Updated Dec 16, 2025Dec 16, 2025

    • Mash

      Public
      Fast genome and metagenome distance estimation using MinHash
      C++
      •
      Other
      •95•451•86•3•Updated Sep 19, 2025Sep 19, 2025

    • Primates

      Public
      Complete assemblies of non-human primate genomes
      Other
      •4•63•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•24•2•0•Updated Dec 17, 2024Dec 17, 2024
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