PathSeq Generate K-mer Library

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DeLuca Lab

• November 16, 2020 16:46

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d) Where do I find (......)?

My apologies for the naive question. I am attempting to run the PathSeq pipeline and am using the pre-built reference files from the Google Bucket (https://console.cloud.google.com/storage/browser/gcp-public-data--broad-references/hg38/v0/CrossSpeciesContamination?pageState=(%22StorageObjectListTable%22:(%22f%22:%22%255B%255D%22))&prefix=&forceOnObjectsSortingFiltering=false). However, I am trying to generate the host k-mer library file and only see a host BWA index image file in the Google Bucket folder. Where do I find the host fasta file that I should use to generate the k-mer library?

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  Genevieve Brandt (she/her)

  • November 17, 2020 21:41

  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

  • November 17, 2020 22:12

  Thanks Genevieve Brandt (she/her)! 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 (she/her)

  • November 19, 2020 19:37

  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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