News:precisionFDA is launching the Truth Challenge V2: Calling Variants from Short and Long Reads in Difficult-to-Map Regions on May 1st!
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2.3 years ago

In the context of whole human genome sequencing, software pipelines typically rely on (1) mapping sequencing reads or assemblies to a reference genome, and (2) the subsequent identification of variants. One way of assessing the performance of such pipelines is by using well-characterized reference datasets such as Genome in a Bottle’s 7 human genome benchmarks. Two of these benchmarks were used in the first precisionFDA Truth Challenge, which assessed variant calling accuracy in “easier-to-map” regions of the genome. The Genome in a Bottle Consortium led by the National Institute of Standards and Technology (NIST) has developed expanded benchmarks for HG003 and HG004, the parents of an Ashkenazi trio. Before their release, precisionFDA and NIST are running a new truth challenge focused on variant calling in more challenging genomic regions.

Join this challenge to assess variant calling pipeline performance on a common frame of reference consisting of difficult-to-map regions, segmental duplications, and the Major Histocompatibility Complex (MHC). Ilumina, PacBio HiFi, and Oxford Nanopore sequencing datasets will be made available for this challenge.

The challenge submission period opens May 1st and runs through June 1st. For more information and to pre-register, visit the challenge site here!

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