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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.

Assembly of a human genome from nanopore sequencing data

January 8, 2017

An international consortium recently released ~30x coverage of a human immortalized cell line (NA12878) sequenced using Oxford Nanopore MinION instruments. Release 3 of this dataset included 39 flowcells, which generated 14,183,584 reads and 91,240,120,433 bases, mostly using the 1D ligation prep, but with a few rapid kit runs as well. Our friends Nick Loman and Jared Simpson asked if we could assemble this data with Canu. Of course we said yes.

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