Shane McCarthy

Using reference-free compressed data structures to analyze sequencing reads from thousands of human genomes

Zamin Iqbal, Jared T. Simpson, Richard Durbin, 2016, bioRxiv.

Crumble: reference free lossy compression of sequence quality values

James K. Bonfield, Richard Durbin, Shane McCarthy, 2018 .

Using BWT structures for reference-free querying of the 1000 Genomes sequence data

Shane McCarthy, Liu Zhicheng, Simpson Jared, 2014 .

How Low Can You Go? Calling Robust ATAC-Seq Peaks Through Read Down-Sampling

Bo Li, Sara Ballouz, Jesse Gillis, 2018 .

Reference-based phasing using the Haplotype Reference Consortium panel

Lukas Forer, Gonçalo R. Abecasis, Richard Durbin, 2016 .

BCFtools/csq: Haplotype-aware variant consequences

Shane McCarthy, Petr Danecek, 2016 .