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

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/