<?xml version="1.0" encoding="UTF-8"?>
<pbds:ReferenceSet
    Name="Human Genome hg38, with Gencode v39 annotations"
    Tags="pacbio,human,hg38,gencode,mas_seq"
    UniqueId="ba3866bf-2aba-7c99-0570-0d6709174e4a"
    Description="This reference contains the human GRCh38/hg38 assembly, plus Gencode v39 annotations"
    CreatedAt="2022-04-04T17:44:41"
    MetaType="PacBio.DataSet.ReferenceSet"
    TimeStampedName="pacbio_dataset_referenceset-220405_004441223"
    Version="3.0.1"
    xmlns:pbbase="http://pacificbiosciences.com/PacBioBaseDataModel.xsd"
    xmlns:pbds="http://pacificbiosciences.com/PacBioDatasets.xsd"
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xsi:schemaLocation="http://pacificbiosciences.com/PacBioDataModel.xsd">
  <!-- Genome data -->
  <pbbase:ExternalResources>
    <pbbase:ExternalResource
        ResourceId="human_GRCh38_no_alt_analysis_set.fasta"
        MetaType="PacBio.ReferenceFile.ReferenceFastaFile"
        UniqueId="649cdc7d-e233-4762-881b-46f368773047"
        TimeStampedName="pacbio_contigfile_contigfastafile-220607_162732195">
      <pbbase:FileIndices>
        <pbbase:FileIndex
            ResourceId="human_GRCh38_no_alt_analysis_set.fasta.fai"
            MetaType="PacBio.Index.SamIndex"
            UniqueId="3794ab44-d4bd-4e84-8f30-7ad794b4ca3c"
            TimeStampedName="pacbio_index_samindex-220607_162732187"/>
      </pbbase:FileIndices>
    </pbbase:ExternalResource>
  </pbbase:ExternalResources>
  <!-- Annotations for this genome used by SMRT Link applications -->
  <pbbase:SupplementalResources>
    <pbbase:ExternalResource
        ResourceId="gencode.v39.annotation.sorted.gtf"
        MetaType="PacBio.ReferenceFile.ReferenceAnnotationFile"
        UniqueId="5fc18043-a9cb-4aeb-81d7-764dc49b638c"
        TimeStampedName="pacbio_referencefile_referenceannotationfile-220607_162732195">
      <pbbase:FileIndices>
        <pbbase:FileIndex
            ResourceId="gencode.v39.annotation.sorted.gtf.pgi"
            MetaType="PacBio.Index.PigeonIndex"
            UniqueId="bee65b9a-42b3-4b7c-9a57-b101dea94489"
            TimeStampedName="pacbio_index_pigeonindex-220607_162732189"/>
      </pbbase:FileIndices>
    </pbbase:ExternalResource>
    <pbbase:ExternalResource
        ResourceId="polyA.list.txt"
        MetaType="PacBio.ReferenceFile.PolyAMotifFile"
        UniqueId="71fcad3b-c45a-47b9-8df4-2a17a99db49e"
        TimeStampedName="pacbio_referencefile_polyamotiffile-220607_162732194"/>
    <pbbase:ExternalResource
        ResourceId="refTSS_v3.3_human_coordinate.hg38.sorted.bed"
        MetaType="PacBio.ReferenceFile.CagePeakFile"
        UniqueId="9a3cae33-96ed-4512-9ce7-5a0c9d5940d4"
        TimeStampedName="pacbio_referencefile_cagepeakfile-220607_162732194">
      <pbbase:FileIndices>
        <pbbase:FileIndex
            ResourceId="refTSS_v3.3_human_coordinate.hg38.sorted.bed.pgi"
            MetaType="PacBio.Index.PigeonIndex"
            UniqueId="3323c7dc-9ebc-46ef-94b3-0aed07422f23"
            TimeStampedName="pacbio_index_pigeonindex-220607_162732193"/>
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    </pbbase:ExternalResource>
    <pbbase:ExternalResource
        ResourceId="intropolis.v1.hg19_with_liftover_to_hg38.tsv.min_count_10.modified2.sorted.tsv"
        MetaType="PacBio.ReferenceFile.IntropolisFile"
        UniqueId="538df2de-50bc-44ec-b82a-63505018ab54"
        TimeStampedName="pacbio_referencefile_intropolisfile-220609_171620434">
      <pbbase:FileIndices>
        <pbbase:FileIndex
            ResourceId="intropolis.v1.hg19_with_liftover_to_hg38.tsv.min_count_10.modified2.sorted.tsv.pgi"
            MetaType="PacBio.Index.PigeonIndex"
            UniqueId="4a21ea1a-fcba-46e0-9d82-0aad63b48a70"
            TimeStampedName="pacbio_index_pigeonindex-220609_171620433"/>
      </pbbase:FileIndices>
    </pbbase:ExternalResource>
  </pbbase:SupplementalResources>
  <pbds:DataSetMetadata>
    <pbds:TotalLength>3099922541</pbds:TotalLength>
    <pbds:NumRecords>195</pbds:NumRecords>
    <pbds:Organism>Homo sapiens</pbds:Organism>
    <pbds:Ploidy>haploid</pbds:Ploidy>
  </pbds:DataSetMetadata>
</pbds:ReferenceSet>