Table 1 PacBio HiFi reads used in evaluation of benchmark.

From: A diploid assembly-based benchmark for variants in the major histocompatibility complex

Instrument

Insert Size

SRA

FTP

Sequel system

10 kb

–

ftp://ftp.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/AshkenazimTrio/HG002_NA24385_son/PacBio_CCS_10kb

Sequel system

15 kb

SRX5327410

ftp://ftp.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/AshkenazimTrio/HG002_NA24385_son/PacBio_CCS_15kb

Sequel II system

11 kb

SRX5527202

ftp://ftp.ncbi.nlm.nih.gov/ReferenceSamples/giab/data/AshkenazimTrio/HG002_NA24385_son/PacBio_SequelII_CCS_11kb

  1. GRCh37 reference used for alignment: ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/phase2_reference_assembly_sequence/hs37d5.fa.gz.
  2. GRCh38 reference used for alignment: ftp://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/000/001/405/GCA_000001405.15_GRCh38/seqs_for_alignment_pipelines.ucsc_ids/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.gz.
  3. https://github.com/PacificBiosciences/pbmm2.
  4. https://github.com/broadinstitute/gatk/releases/tag/4.0.10.1.
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