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shajoezhu / NA12878

Data and analysis for NA12878 genome on nanopore

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NA12878 Human Reference on Oxford Nanopore MinION

Contributors

Mark Akeson (1), Andrew D. Beggs (2), Thomas Nieto (2), Miten Jain (1), Nicholas J. Loman (3), Matt Loose (4), Sunir Malla (4), Justin O’Grady (5), Hugh E. Olsen (1), Josh Quick (3), Hollian Richardson (5), Jared T. Simpson (6,7), Terrance P. Snutch (8), Louise Tee (2), John R. Tyson (8)

  1. University of California, Santa Cruz, Santa Cruz, CA, USA
  2. University of Birmingham, Birmingham, B15 2TT
  3. Institute of Microbiology and Infection, School of Biosciences, University of Birmingham, Birmingham, B15 2TT, United Kingdom
  4. DeepSeq, School of Life Sciences, University of Nottingham, Nottingham, UK
  5. Norwich Medical School, University of East Anglia, Norwich, NR4 7UQ, United Kingdom.
  6. Ontario Institute for Cancer Research, Toronto, Canada
  7. Department of Computer Science, University of Toronto, Toronto, Canada
  8. Michael Smith Laboratories, University of British Columbia, Vancouver, Canada

Background

We have sequenced the CEPH1463 (NA12878/GM12878, Ceph/Utah pedigree) human genome reference standard on the Oxford Nanopore MinION using 1D ligation kits (450 bp/s) using R9.4 chemistry (FLO-MIN106).

Human genomic DNA from GM12878 human cell line (Ceph/Utah pedigree) was either purchased from Coriell - "DNA" - (cat no NA12878) or extracted from the cultured cell line - "cells". As the DNA is native, modified bases will be preserved.

Data availability

Check back in the next few days for the remaining reads, alignments and raw signal-level reads.

rel2

We have processed approximately 2/3rds of the total dataset.

The current release rel2 consists of:

  • 25 flowcells
  • 58958035887 bases
  • 9053909 reads
flowcell_id reads bases Date Centre SampleType Links Link
FAB39075 466324 2439308482 20/09/16 UBC DNA FASTQ BAM
FAB39043 305667 1543725551 23/09/16 Bham DNA FASTQ BAM
FAB42706 400751 1857323339 12/10/16 UBC DNA FASTQ BAM
FAB42316 107013 606761274 14/10/16 Notts DNA FASTQ BAM
FAB42205 312666 1664297400 14/10/16 Notts DNA FASTQ BAM
FAB42561 231562 1510037000 19/10/16 Notts DNA FASTQ BAM
FAB42473 598480 3140575707 20/10/16 UBC DNA FASTQ BAM
FAB42476 376897 2061807133 27/10/16 UBC DNA FASTQ BAM
FAB42451 769524 4256154457 28/10/16 Notts DNA FASTQ BAM
FAB42704 276151 1750146174 28/10/16 UBC DNA FASTQ BAM
FAB42810 265456 1665251718 02/11/16 Norwich DNA FASTQ BAM
FAB46683 72602 286264094 17/11/16 Bham DNA FASTQ BAM
FAB45332 530913 2863965040 17/11/16 UBC DNA FASTQ BAM
FAB43577 241646 1423672212 18/11/16 UCSC DNA FASTQ BAM
FAB44989 558195 3443623448 18/11/16 UCSC DNA FASTQ BAM
FAF01169 16489 120873419 22/11/16 Bham Cells FASTQ BAM
FAF01441 43281 358912895 22/11/16 Bham Cells FASTQ BAM
FAB45277 53541 445614920 22/11/16 Notts Cells FASTQ BAM
FAB45321 299172 2583989736 22/11/16 Notts Cells FASTQ BAM
FAF01132 689781 5455971336 25/11/16 Bham Cells FASTQ BAM
FAF01127 632728 4972081712 25/11/16 Bham Cells FASTQ BAM
FAB49712 592317 4589575564 28/11/16 Bham Cells FASTQ BAM
FAF01253 442221 3476220233 28/11/16 Bham Cells FASTQ BAM
FAB49914 309162 2840857895 28/11/16 Notts Cells FASTQ BAM
FAB45271 461370 3601025148 28/11/16 Notts Cells FASTQ BAM

Please verify downloads against MD5 hashes and list of links.

Alignments

Reads aligned against pre-computed 1000 genomes GRCh38 BWA database at ftp://ftp-trace.ncbi.nih.gov/1000genomes/ftp/technical/reference/GRCh38_reference_genome/ with decoys using BWA MEM (commit: 5961611c358e480110793bbf241523a3cfac049b) using parameters -x ont2d. Alignment statistics calculated using samtools stats (samtools version 1.3.1).

FlowcellID Sequences Mapped Mapped.MQ0 Unmapped Bases.Mapped Avg.Length Link
FAB39075 466325 425113 28167 41212 2146410660 5230 BAM
FAB39043 305667 294755 13692 10912 1457990655 5050 BAM
FAB42706 400751 353625 15675 47126 1776803301 4634 BAM
FAB42316 107013 95753 3137 11260 586781780 5669 BAM
FAB42205 312666 278495 12223 34171 1582844105 5322 BAM
FAB42561 231562 223447 10030 8115 1412971869 6521 BAM
FAB42473 598480 571453 28466 27027 2929628858 5247 BAM
FAB42476 376897 364557 17046 12340 1953918702 5470 BAM
FAB42451 769524 738272 33281 31252 3963057878 5530 BAM
FAB42704 276151 263721 12926 12430 1619871937 6337 BAM
FAB42810 265456 251084 14164 14372 1483597856 6273 BAM
FAB46683 72602 64736 5306 7866 269203835 3942 BAM
FAB45332 530913 497838 26391 33075 2620591926 5394 BAM
FAB43577 241646 231695 11028 9951 1321809290 5891 BAM
FAB44989 558195 536543 25934 21652 3161714885 6169 BAM
FAF01169 16489 15772 710 717 114528983 7330 BAM
FAF01441 43281 41775 1847 1506 335717952 8292 BAM
FAB45277 53541 51951 2132 1590 426614901 8322 BAM
FAB45321 299172 283353 15165 15819 2365977206 8637 BAM
FAF01132 689781 655357 33564 34424 4966810089 7909 BAM
FAF01127 632728 605633 27192 27095 4640355789 7858 BAM
FAB49712 592317 576236 24321 16081 4308054580 7748 BAM
FAF01253 442221 428640 18700 13581 3245588740 7860 BAM
FAB49914 309162 296238 12280 12924 2673699794 9188 BAM
FAB45271 461370 440262 19535 21108 3388203702 7805 BAM

Please verify downloads against MD5 hashes.

Read lengths

Cellular library read length distribution

Figure: A typical read length distribution from a flowcell where we have run a cell-extracted DNA library. The y-axis shows the count of bases. Mean read length ~8.6kb with N50 of ~12.5kb (vertical line). Reads longer than 60kb are not expected due to limitations of the QIAGEN extraction kit employed.

Disclaimer

This dataset is currently subject to rapid change as we continue to post up runs, therefore some statistics here may not represent full nanopore runs.

Acknowledgements

We would like to acknowledge the support of Oxford Nanopore Technologies in generating this dataset, with particular thanks to Rosemary Dokos, Oliver Hartwell, Jonathan Pugh and Clive Brown. We would like to thank Radoslaw Poplawski and Simon Thompson for technical assistance with configuration and optimising of the CLIMB platform file system.

Contact

Please raise issues on this Github repository concerning this dataset. A preprint describing the dataset in more detail will be available shortly.

History

* rel1: 1st December 2016. Initial release.

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Data and analysis for NA12878 genome on nanopore