Research

Papers

For a complete and up-to-date publication list, so the Google Scholar profile.

Software

Alignment

  • Bowtie – fast short read alignment
  • Bowtie 2 – fast gapped read alignment for short reads
  • Qtip – mapping quality predictions
  • Samovar – somatic mosaic variant detection
  • Vargas – heuristic-free read alignment
  • Arioc by Richard Wilton – fast GPU-based alignment
  • HISAT by Daehwan Kim – fast spliced alignment

Pangenome Indexing and Alignment

  • FORGe – selecting variation to include in a pangenome
  • Reference Flow – multi-genome alignment
  • r-index – by Nicola Prezza with modifications by Taher Mun, pangenome index
  • MONI – by Max Rossi, fast MEM finding with a pangenome index
  • SPUMONI – fast classification with a pangenome index
  • rowbowt – efficient pangenome genotyping
  • LevioSAM – lift-over for pangenome alignment
  • LevioSAM 2 – pangenome alignment across structurally distinct assemblies

Genomic Sketching

  • Dashing – genomic sketching with HyperLogLog
  • Dashing 2 – genomic sketching with SetSketch
  • DandD – k-independent measurement of sequence content & similarity

Large-scale Reanalysis

  • recount3 – vast compendium of analyzed, summarized RNA-seq experiments
  • Snaptron – queryable index over recount
  • ASCOT by Jonathan Ling – catalog of cell type specific splicing
  • FC-R2 by Eddie Imada & Diego Fernando Sanchez – recount data analyzed with FANTOM annotations
  • REPAC by Eddie Imada – catalog of alternate polyadenylation
  • (superseded) Rail-dbGaP
  • (superseded) recount2
  • (superseded) recount
  • (superseded) Intropolis
  • (superseded) Myrna
  • (superseded) Crossbow

RNA-seq analysis

  • Monorail – reproducible recount3 analysis pipeline
  • Megadepth – RNA-seq coverage analysis
  • Polyester by Alyssa Frazee – RNA-seq read simulator
  • Boiler – compression of RNA-seq alignments
  • (superseded) Rail-RNA

Other

  • Samovar – somatic mosaic variant detection
  • Lighter by Li Song – short read error correction
  • minicore – fast k-means clustering
  • Bsmooth – bisulfity sequencing data analysis