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Software

Here is the list of open-source documented software hosted on GitHub that my lab developed or co-developed. Some of these are being actively maintained and used by 1000+ users.

  • RAFT - Improves long read assembly by proper treatment of contained reads
    Code

  • Minichain - Long-read aligner to pangenome graphs
    Code

  • PanAligner - Long-read aligner to cyclic pangenome graphs
    Code

  • Winnowmap - Long read (ONT/PacBio) mapper using weighted minimizer sampling technique
    Code

  • Mashmap - fast approximate mapper for long DNA sequences (e.g., reads, contigs) using LSH
    Code

  • FastANI - fast whole-genome similarity (ANI) estimator
    Code

  • VF - Provably-good algorithms for variant filtering in genome graphs
    Code

  • ChainX - Optimal co-linear anchor chaining algorithm
    Code

  • Metamaps - strain-level metagenomics analysis for long reads
    Code

  • PaSGAL - parallel (multicore-SIMD) long/short reads to pan-genome graph (DAG) alignment
    Code

  • ParConnect - distributed-memory parallel connected components solver for massive graphs
    Code

  • PairG - index builder for validating paired-end alignment distance constraints in pan-genome graphs
    Code

  • Kmerind - Parallel k-mer indexing for biological sequences
    Code