Nanopore sequencing, Shasta toolkit enable de novo assembly of 11 human genomes

Re:Nanopore sequencing, Shasta toolkit enable de novo assemb... by zmmmmm on Tuesday May 05, 2020 @09:07PM (#23086933)

It's a bit frustrating (and concerning?) that their data repository [1] seems incomplete; the most important seqences (GM12878 / HG001) are missing from everything but the raw data directory. This is the sample that most laboratories would likely have readily available for comparison to their results, but for some reason they have omitted to deposit their final results for it (unless I'm missing something ...).

[1] https://s3-us-west-2.amazonaws.com/human-pangenomics/index.h...

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Re:Nanopore sequencing, Shasta toolkit enable de novo assemb... by vikramkr on Tuesday May 05, 2020 @10:10PM (#23087287)

Is it in any of the supplementary information or in any of the figure source data links in the paper? They do link in addition to the AWS open data this link (https://www.ebi.ac.uk/ena/data/search?query=PRJEB37264) - did you look through that? Other than that now idea - seems like a bit of an oversight from nature if they wouldn't make sure important sequences were readily available, you'd imagine they'd be important for peer review as well prior to publication.

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Re:Nanopore sequencing, Shasta toolkit enable de novo assemb... by terrakota on Tuesday May 05, 2020 @10:42PM (#23087456)

Look at their "sample selection" section. "The goal of sample selection was to select a set of individuals that collectively captured the maximum amount of weighted allelic diversity53." And also says "We also added the three Ashkenazim Trio samples and the Puerto Rican individual (HG00733). These four samples were added for the purposes of comparison with other studies that are using them."

Four genomes make a comprehensive evaluation set, don't think HG001 is "absolutely" needed.

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