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    14 repositories

    • PHI

      Public
      Pangenome graph-based genome inference
      Python
      •
      Other
      •1•6•1•0•Updated Mar 7, 2025Mar 7, 2025

    • at-cg.github.io

      Public
      PI/Lab website
      SCSS
      •
      MIT License
      •1•2•0•0•Updated Mar 7, 2025Mar 7, 2025

    • Hands-On-Tutorials

      Public
      Hands-on demo for various algorithmic concepts associated with biological sequence analysis
      0•2•0•0•Updated Feb 11, 2025Feb 11, 2025

    • phenotypeCR

      Public
      HPO-based phenotype concept recognition using language models
      Jupyter Notebook
      •0•1•0•0•Updated Jan 30, 2025Jan 30, 2025

    • mm2-plus

      Public
      Fast long-read mapper and whole-genome aligner (accelerated version of minimap2)
      C
      •
      Other
      •2•29•0•0•Updated Dec 30, 2024Dec 30, 2024

    • DiploidGenomeAssembly

      Public
      C++
      •0•0•0•0•Updated Dec 21, 2024Dec 21, 2024

    • CGProb

      Public
      Counting coverage gaps
      C++
      •1•3•0•0•Updated Oct 4, 2024Oct 4, 2024

    • RAFT

      Public
      genome-assemblylong-reads
      C++
      •1•22•2•0•Updated Aug 22, 2024Aug 22, 2024

    • minichain

      Public
      Long-read aligner to pangenome graphs
      alignmentpangenomicslong-reads
      C
      •
      Other
      •3•26•1•0•Updated May 20, 2024May 20, 2024

    • PanAligner

      Public
      Long read aligner for cyclic and acyclic pangenome graphs
      pangenomevariation-graphsread-alignment
      C
      •
      Other
      •4•36•3•0•Updated Dec 20, 2023Dec 20, 2023

    • containX

      Public
      Contained read analysis for string graph construction during de novo genome assembly
      C++
      •1•5•0•0•Updated Apr 5, 2023Apr 5, 2023

    • MMC

      Public
      Minimizer counting and analysis
      kmer-countingminimizersbioinformatics
      C++
      •1•2•0•0•Updated Oct 7, 2022Oct 7, 2022

    • ChainX

      Public
      Anchor chaining method for nucleotide sequences
      C++
      •
      Apache License 2.0
      •3•8•1•0•Updated Mar 22, 2022Mar 22, 2022

    • VF

      Public
      Variant selection framework in genome graphs
      C++
      •
      MIT License
      •0•4•0•0•Updated Oct 14, 2021Oct 14, 2021