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NCBI-Codeathons / super-minityper

Long Read SVs
MIT License
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Link to data #1

Closed edawson closed 5 years ago

edawson commented 5 years ago

We need links to several data sets:

  1. SV calls and graph for human data, + matched reads

Suggestion: GIAB HG002

  1. Metagenome readset containing structural variants (e.g. E. coli or yeast)

Mock microbial is one possibility: https://github.com/LomanLab/mockcommunity

edawson commented 5 years ago

GIAB HG002 variant calls: ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/analysis/NIST_SVs_Integration_v0.6/HG002_SVs_Tier1_v0.6.vcf.gz

Uploaded as unzipped VCF to dnanexus

tijyojwad commented 5 years ago

I'm upload the loman lab dataset. might take a while coz it's large and downloading it first onto the worker machine is taking a while

Fu-Yilei commented 5 years ago

SRR7415638 is a metagenome dataset of Saccharomyces cerevisiae. https://lomanlab.github.io/mockcommunity/