Oxford Nanopore PromethION whole-genome sequencing of seven Genome in a Bottle (GIAB) human reference samples
Long-read whole-genome sequencing of the seven NIST Genome in a Bottle (GIAB) human reference samples, generated by the Mason Lab at Weill Cornell Medicine to benchmark Oxford Nanopore variant calling and 5mC methylation detection against the GIAB truth sets.  Samples comprise the three GIAB reference trios and the CEPH/Utah reference individual: HG001 (NA12878, CEPH/Utah); the Ashkenazi trio HG002 (NA24385, son), HG003 (NA24149, father) and HG004 (NA24143, mother); and the Han Chinese trio HG005 (NA24631, son), HG006 (NA24694, father) and HG007 (NA24695, mother). All are Coriell cell lines distributed by NIST for open benchmarking use.  Genomic DNA was sequenced on an Oxford Nanopore PromethION (device PCT0080, R9.4.1 flow cells) in 2019. This study comprises the raw nanopore signal data, deposited as multi-read FAST5 so that the reads can be re-basecalled with current models independently of the basecalls available at the time of sequencing. Six samples were sequenced on the same device across adjacent flow cell positions; HG002 was sequenced on a separate flow cell (PAD29551).  Read totals per sample, from the per-read sequencing summaries, are 8,002,953 (HG001), 17,976,441 (HG003), 17,624,047 (HG004), 24,151,846 (HG005), 20,331,349 (HG006) and 24,425,946 (HG007), totalling approximately 5.6 TB of raw signal.  Data originally written as single-read FAST5 was converted to multi-read FAST5 before deposition. The conversion was verified lossless by three independent checks: read counts reconciled against the per-read sequencing summaries, read-ID set equality between input and output, and byte-level comparison of raw signal arrays for sampled reads.  The HG007 archive contains 24,425,946 reads, which is a uniformly distributed subset of the 27,458,774 reads described by that run's sequencing summaries; the absent reads span the full run duration and channel set and match the overall pass/fail ratio, and were already absent from the source archive.
Long-read whole-genome sequencing of the seven NIST Genome in a Bottle (GIAB) human reference samples, generated by the Mason Lab at Weill Cornell Medicine to benchmark Oxford Nanopore variant calling and 5mC methylation detection against the GIAB truth sets.  Samples comprise the three GIAB reference trios and the CEPH/Utah reference individual: HG001 (NA12878, CEPH/Utah); the Ashkenazi trio HG002 (NA24385, son), HG003 (NA24149, father) and HG004 (NA24143, mother); and the Han Chinese trio HG005 (NA24631, son), HG006 (NA24694, father) and HG007 (NA24695, mother). All are Coriell cell lines distributed by NIST for open benchmarking use.  Genomic DNA was sequenced on an Oxford Nanopore PromethION (device PCT0080, R9.4.1 flow cells) in 2019. This study comprises the raw nanopore signal data, deposited as multi-read FAST5 so that the reads can be re-basecalled with current models independently of the basecalls available at the time of sequencing. Six samples were sequenced on the same device across adjacent flow cell positions; HG002 was sequenced on a separate flow cell (PAD29551).  Read totals per sample, from the per-read sequencing summaries, are 8,002,953 (HG001), 17,976,441 (HG003), 17,624,047 (HG004), 24,151,846 (HG005), 20,331,349 (HG006) and 24,425,946 (HG007), totalling approximately 5.6 TB of raw signal.  Data originally written as single-read FAST5 was converted to multi-read FAST5 before deposition. The conversion was verified lossless by three independent checks: read counts reconciled against the per-read sequencing summaries, read-ID set equality between input and output, and byte-level comparison of raw signal arrays for sampled reads.  The HG007 archive contains 24,425,946 reads, which is a uniformly distributed subset of the 27,458,774 reads described by that run's sequencing summaries; the absent reads span the full run duration and channel set and match the overall pass/fail ratio, and were already absent from the source archive.