Sequel II System Data Release: HG002 SV and SNVs (HiFi Reads powered by CCS)

SAMPLE

GIAB HG002 extracted DNA

METHODS

• Shearing 15 kb with Megaruptor
• Library prep TPK 1.0
• Size selection Fraction 4 (11kb) with Sage ELF
• Sequencing Sequel System II with "Early Access" binding kit (101-490-800) and chemistry (101-490-900)
• Run time 12 hour pre-extension; 30 hour movie
• CCS SMRTLink 6.1 "Early Access" Circular Consensus Sequence Analysis (ccs v3.2.1)
• Reference hs37d5 (GRCh37 with decoy)
• Alignment pbmm2 --preset CCS
• Variant Calling GATK v4.0.10.1 HaplotypeCaller
• Variant Phasing WhatsHap v0.17

FOLDERS

• subreads Basecalled reads and metadata for three Sequel II SMRTCells 8M loaded with 11kb HG002 libraries
• consensusreads Circular Consensus reads and metadata for runs above
• consensusalignments CCS reads above, aligned to hs37d5 with pbmm2.
• gatk4hc Small variants called with GATK4 HaplotypeCaller and phased with WhatsHap

• •     /GIAB_small_variant_v3.3.2_benchmark  Benchmarked against GIAB small variant v3.3.2 with hap.py
    

•     * /GIAB_phasing_benchmark               Benchmarked against 10X/Trio phased variant set.
  

• pbsv Structural variants called with SMRT Link Structural Variant Calling (powered by pbsv)

•     /truvari-giab-v0.6                    Benchmarked against GIAB structural variant v0.6 with Truvar
  

DOWNLOAD

URLs and md5 checksums are listed in URLs.txt

Note: subreads directory is 1.2 TB and contains the basecalled Sequel II data (unaligned BAM file format)

Download Data: https://downloads.pacbcloud.com/public/dataset/HG002_SV_and_SNV_CCS/