Repositories list

• billi

  Public
  Enumerating bubbles in pangenome graphs

  bioinformaticsbubblespangenomics

  bioinformaticsbubblespangenomics

  C++

  •0•15•0•0•Updated Apr 1, 2026Apr 1, 2026

• at-cg.github.io

  Public
  PI/Lab website

  SCSS

  •

  MIT License

  •1•2•0•0•Updated Mar 11, 2026Mar 11, 2026

• Hands-On-Tutorials

  Public
  Hands-on demo for various algorithmic concepts associated with biological sequence analysis

  0•2•0•0•Updated Mar 11, 2026Mar 11, 2026

• HALE

  Public
  Error correction of long reads

  nanoporeassemblypacbio+ 3

  nanoporeassemblypacbiolong-readserror-correctionploidy

  Rust

  •0•13•0•0•Updated Jan 30, 2026Jan 30, 2026

• NanoLabel

  Public
  Fast and accurate signal classifier for nanopore sequencing

  bioinformaticssupervised-learningxgboost+ 3

  bioinformaticssupervised-learningxgboostoxford-nanoporetargeted-sequencingadaptive-sampling

  Python

  •0•0•0•0•Updated Jan 26, 2026Jan 26, 2026

• mm2-plus

  Public
  Fast long-read mapper and whole-genome aligner (accelerated version of minimap2)

  C

  •

  Other

  •2•59•0•0•Updated Jan 7, 2026Jan 7, 2026

• ChainX

  Public
  Anchor chaining method for nucleotide sequences

  C++

  •

  Apache License 2.0

  •4•8•1•0•Updated Dec 15, 2025Dec 15, 2025

• ds221-2025

  Public
  This repository is for DS221 assignments

  C++

  •4•1•0•0•Updated Sep 17, 2025Sep 17, 2025

• PHI

  Public
  Pangenome graph-based genome inference

  Python

  •

  Other

  •1•13•1•0•Updated Jul 24, 2025Jul 24, 2025

• GenomeRepeatStats

  Public
  C++

  •0•1•0•0•Updated Jun 24, 2025Jun 24, 2025

• phenotypeCR

  Public
  HPO-based phenotype concept recognition using language models

  Jupyter Notebook

  •0•1•0•0•Updated Jan 30, 2025Jan 30, 2025

• CGProb

  Public
  Counting coverage gaps

  C++

  •1•3•0•0•Updated Oct 4, 2024Oct 4, 2024

• RAFT

  Public
  Improved long-read assembly by preserving contained reads

  genome-assemblylong-reads

  genome-assemblylong-reads

  C++

  •1•30•3•0•Updated Aug 22, 2024Aug 22, 2024

• minichain

  Public
  Long-read aligner to pangenome graphs

  alignmentpangenomicslong-reads

  alignmentpangenomicslong-reads

  C

  •

  Other

  •3•29•1•0•Updated May 20, 2024May 20, 2024

• PanAligner

  Public
  Long read aligner for cyclic and acyclic pangenome graphs

  pangenomevariation-graphsread-alignment

  pangenomevariation-graphsread-alignment

  C

  •

  Other

  •4•40•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

  bioinformaticskmer-countingminimizers

  bioinformaticskmer-countingminimizers

  C++

  •1•3•0•0•Updated Oct 7, 2022Oct 7, 2022

• VF

  Public
  Variant selection framework in genome graphs

  C++

  •

  MIT License

  •0•4•0•0•Updated Oct 14, 2021Oct 14, 2021