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Variant Discovery in High-Throughput Sequencing Data

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Developed in the Data Sciences Platform at the Broad Institute, the toolkit offers a wide variety of tools with a primary focus on variant discovery and genotyping. Its powerful processing engine and high-performance computing features make it capable of taking on projects of any size. Learn more

PathSeq Generate K-mer Library

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    Genevieve Brandt

    Hi DeLuca Lab,

    I am not sure you need that file:

    "Users can download recommended pre-built reference files for use with PathSeq from the Broad's 'gcp-public-data' Google Bucket. This tutorial also covers how to build custom host and microbe references."

    In the tutorial, it is shown how to generate the k-mer library from custom files, but for the tutorial, you can download the pre-made library files.

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    DeLuca Lab

    Thanks Genevieve Brandt! I was looking in the Google Bucket and did not see a .hss file which was used in the tutorial. Can I use the .bfi file as the k-mer library?

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    Genevieve Brandt

    Hi DeLuca Lab, you can build the k-mer library using PathSeqBuildKmers with the files that are available in the Google Bucket. Hope this helps!

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