Genome Informatics Section


Fast and highly accurate HLA typing by linearly-seeded graph alignment

March 22, 2017

HLA*PRG:LA approximates the graph alignment process by starting with linear sequence alignments. It brings down the resource requirements per sample for the HLA typing process to 30GB RAM/30 CPU hours, and produces highly accurate calls.

Single-molecule sequencing and chromatin conformation capture enable de novo reference assembly

March 6, 2017

After a long and fruitful collaboration with our friends at the USDA, we have finally published the goat genome in Nature Genetics. “We demonstrate current state of the art for de novo assembly using the domestic goat (Capra hircus) based on long reads for contig formation, short reads for consensus validation, and scaffolding by optical and chromatin interaction mapping. These combined technologies produced what is, to our knowledge, the most continuous de novo mammalian assembly to date, with chromosome-length scaffolds and only 649 gaps.” If you hit the paywall, you can read the preprint for free on bioRxiv, and NHGRI did a nice piece on the backstory. Huge credit to co-first authors Derek Bickhart, Ben Rosen, and Sergey Koren for years of hard work on this project.



A single molecule sequence assembler for genomes large and small


Fast genome and metagenome distance estimation using MinHash
Single-molecule sequencing and conformational capture enable de novo mammalian reference genomes
Nature Genetics, March 16, 2017
Bickhart DM … Koren SPhillippy AM … Smith TPL