Skip to content

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

tkerelska edited this page Mar 13, 2019 · 8 revisions


GIAB HG002 extracted DNA


  • 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 SMRT Link v6.1.0 "Early Access" Circular Consensus Sequence Analysis (ccs v3.2.1)
  • SV Calling SMRT Link v6.1.0 "Early Access" Structural Variant Calling (powered by pbsv)
  • Alignment pbmm2 --preset CCS
  • Variant Calling GATK v4.0.10.1 HaplotypeCaller
  • Variant Phasing WhatsHap v0.17
  • Reference hs37d5 (GRCh37 with decoy)


  • 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 /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


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:

Clone this wiki locally
You can’t perform that action at this time.
You signed in with another tab or window. Reload to refresh your session. You signed out in another tab or window. Reload to refresh your session.