gtgseq

ONT R10.4.1 5kHz chemistry - DNA data

Make sure to first go through the directory structure, file name conventions and downloading method documented here.

Table of Contents

• ONT R10.4.1 5kHz chemistry - DNA data
  • NA24385 (HG002) PromethION data (~40X, longer reads, enzyme E8.2.1)
  • NA24385 (HG002) PromethION data (~40X)
  • NA24385 (HG002) PromethION data (~20X)
• ONT RNA004 chemistry - RNA data
  • UHR PromethION data
• ONT R10.4.1 4kHz chemistry - DNA data
  • NA24385 (HG002) PromethION data (~30X)
  • NA12878 (HG001) PromethION data (~20X)

NA24385 (HG002) PromethION data (~40X, longer reads, enzyme E8.2.1)

• Info: HG002 (Coriell Institute, GM24385) was cultured in RPMI1640 (Gibco, 11875093) with 15% fetal bovine serum (Bovogen, SFBS-AU) at 37°C with 5% CO2. DNA was extracted using Nanobind CBB kit (PacBio, 102-301-900). DNA was sheared to ~65 kb using the Megaruptor 3 (Diagenode) and fragments <10 kb were removed using SRE kit (PacBio, 102-208-300). Libraries prepared using SQK-LSK114 (with enzyme E8.2.1) and sequenced on a R10.4.1 flow cell (Oxford Nanopore Technologies) at 5kHz sampling rate.

• Notes: the complete dataset with 6.9M reads (119.5 Gbases).
• Reads lengths: 9.0 kbases median, 17.2 kbases mean, 697.4 kbases max
• Browse: https://gtgseq.s3.amazonaws.com/index.html#ont-r10-5khz-dna/NA24385_e821/

raw signal data:

• BLOW5 file
  • direct link: PGXXSX240470_reads.blow5
  • s3 location: s3://gtgseq/ont-r10-5khz-dna/NA24385_e821/raw/PGXXSX240470_reads.blow5
  • md5sum: ebc003e549870344e194ea624813dd3e
• BLOW5 index
  • direct link: PGXXSX240470_reads.blow5.idx
  • s3 location: s3://gtgseq/ont-r10-5khz-dna/NA24385_e821/raw/PGXXSX240470_reads.blow5.idx
  • md5sum: 3e7ef8627f2179e77510699552680f02
• Also available on ENA: ERR14751980

basecalls:

• Dorado 0.8.3 super accuracy
  • basecalled with Dorado 0.8.3 through slow5-dorado.
  • model: dna_r10.4.1_e8.2_400bps_sup@v5.0.0
  • only reads that passed the qscore filter threshold 10 are included
    • FASTQ: PGXXSX240470_dorado083sup.fastq.gz
    • FASTQ index: PGXXSX240470_dorado083sup.fastq.gz.gzi and PGXXSX240470_dorado083sup.fastq.gz.fai
    • FASTQ is also available on ENA: ERR14758575
  • mapped with minimap2 2.26 against hg38noAlt with map-ont preset
    • BAM: PGXXSX240470_dorado083sup_mm226.bam
    • BAM index: PGXXSX240470_dorado083sup_mm226.bam.bai

modcalls

• f5c 1.5 CpG methylation frequencies
  • PGXXSX240470_dorado083sup_mm226.bam and PGXXSX240470_dorado083sup.fastq.gz used as input
  • bgzip compressed methylation freqencies: PGXXSX240470_dorado083sup_mm226_f5c15_mfreq.tsv.gz

NA24385 (HG002) PromethION data (~40X)

• Info: HG002 (Coriell Institute, GM24385) was cultured in RPMI1640 (Gibco, 11875093) with 15% fetal bovine serum (Bovogen, SFBS-AU) at 37°C with 5% CO2. DNA was extracted using Nanobind CBB kit (PacBio, 102-301-900). DNA was sheared to ~33 kb using the Megaruptor 3 (Diagenode) and libraries prepared using SQK-LSK114 and sequenced on a R10.4.1 flow cell (Oxford Nanopore Technologies) at 5kHz sampling rate to generate ~40X genome coverage.
• Notes: the complete dataset with 18.8M reads (130.494 Gbases).
• Reads lengths: 2.7 kbases median, 6.9 kbases mean, 854.8 kbases max
• Browse: https://gtgseq.s3.amazonaws.com/index.html#ont-r10-5khz-dna/NA24385_2/

raw signal data:

• BLOW5 file
  • direct link: PGXXSX240041_reads.blow5
  • s3 location: s3://gtgseq/ont-r10-5khz-dna/NA24385_2/raw/PGXXSX240041_reads.blow5
  • md5sum: b9e0f4fc49ffe4d1e39dc9c09eccdeac
• BLOW5 index
  • direct link: PGXXSX240041_reads.blow5.idx
  • s3 location: s3://gtgseq/ont-r10-5khz-dna/NA24385_2/raw/PGXXSX240041_reads.blow5.idx
  • md5sum: 18ac205e53552bcb561ea5b3a55cd9b7
• Also available on ENA: ERR12997168

basecalls:

• Guppy 6.5.7 high accuracy
  • basecalled with Guppy 6.5.7 through buttery-eel.
  • model: dna_r10.4.1_e8.2_400bps_5khz_hac_prom.cfg
  • only reads that passed the qscore filter threshold 9 are included
    • FASTQ: PGXXSX240041_guppy657hac.fastq.gz
    • FASTQ index: PGXXSX240041_guppy657hac.fastq.gz.gzi and PGXXSX240041_guppy657hac.fastq.gz.fai
  • mapped with minimap2 2.26 against hg38noAlt with map-ont preset
    • BAM: PGXXSX240041_guppy657hac_mm226.bam
    • BAM index: PGXXSX240041_guppy657hac_mm226.bam.bai

modcalls

• f5c 1.3 CpG methylation frequencies
  • PGXXSX240041_guppy657hac_mm226.bam and PGXXSX240041_guppy657hac.fastq.gz used as input
  • bgzip compressed methylation freqencies: PGXXSX240041_guppy657hac_mm226_f5c13_mfreq.tsv.gz

NA24385 (HG002) PromethION data (~20X)

• Info: sheared DNA libraries (~25Kb) were prepared using the ONT LSK114 ligation library prep and a R10.4.1 flow cell at 5kHz sampling rate was used to generate ~20X genome coverage.
• Notes: the complete dataset with 12.5M reads (51.211 Gbases).
• Reads lengths: 1.5 kbases median, 4.1 kbases mean, 288.9 kbases max
• Browse: https://gtgseq.s3.amazonaws.com/index.html#ont-r10-5khz-dna/NA24385/

raw signal data:

• BLOW5 file
  • direct link: PGXXXX230339_reads.blow5
  • s3 location: s3://gtgseq/ont-r10-5khz-dna/NA24385/raw/PGXXXX230339_reads.blow5
  • md5sum: 2dab2e0c042b0fb5f9f3794c7c916420
• BLOW5 index
  • direct link: PGXXXX230339_reads.blow5.idx
  • s3 location: s3://gtgseq/ont-r10-5khz-dna/NA24385/raw/PGXXXX230339_reads.blow5.idx
  • md5sum: 84a1b5317f0e92f73143070481df8fe3
• Also available on ENA: ERR12997167

basecalls:

• Guppy 6.5.7 high accuracy
  • basecalled with Guppy 6.5.7 through buttery-eel.
  • model: dna_r10.4.1_e8.2_400bps_5khz_hac_prom.cfg
  • only reads that passed the qscore filter threshold 9 are included
    • FASTQ: PGXXXX230339_guppy657hac.fastq.gz
    • FASTQ index: PGXXXX230339_guppy657hac.fastq.gz.gzi and PGXXXX230339_guppy657hac.fastq.gz.fai
  • mapped with minimap2 2.26 against hg38noAlt with map-ont preset
    • BAM: PGXXXX230339_guppy657hac_mm226.bam
    • BAM index: PGXXXX230339_guppy657hac_mm226.bam.bai

modcalls

• f5c 1.3 CpG methylation frequencies
  • PGXXXX230339_guppy657hac_mm226.bam and PGXXXX230339_guppy657hac.fastq.gz used as input
  • bgzip compressed methylation freqencies: PGXXXX230339_guppy657hac_mm226_f5c13_mfreq.tsv.gz

ONT RNA004 chemistry - RNA data

UHR PromethION data

• Info: Universal human reference RNA (300 ng polyA enriched RNA) was prepared using the SQK-RNA004 kit from Nanopore. Prepared library (48 ng) was loaded onto a FLO-PRO004RA flow cell.
• Notes: the complete dataset with 15.4M reads (17.554 Gbases).
• Reads lengths: 864 bases median, 1.137 kbases mean, 321 kbases max
• Browse: https://gtgseq.s3.amazonaws.com/index.html#ont-rna004-rna/UHR/

raw signal data:

• BLOW5 file
  • direct link: PNXRXX240011_reads.blow5
  • s3 location: s3://gtgseq/ont-rna004-rna/UHR/raw/PNXRXX240011_reads.blow5
  • md5sum: 671be5b88f2b54a9e22ced351493b7a9
• BLOW5 index
  • direct link: PNXRXX240011_reads.blow5.idx
  • s3 location: s3://gtgseq/ont-rna004-rna/UHR/raw/PNXRXX240011_reads.blow5.idx
  • md5sum: e3ea326d300a22008e2821ce10d17649
• Also available on ENA: ERR12997170

basecalls:

• Dorado server 7.2.13 super accuracy
  • basecalled with Dorado server 7.2.13 through buttery-eel.
  • model: rna_rp4_130bps_sup.cfg
  • only reads that passed the qscore filter threshold 10 are included
    • FASTQ: PNXRXX240011_dorado7213sup.fastq.gz
    • FASTQ index: PNXRXX240011_dorado7213sup.fastq.gz.gzi and PNXRXX240011_dorado7213sup.fastq.gz.fai
  • mapped with minimap2 2.26 against gencode.v40.transcripts with map-ont preset and -uf
    • BAM: PNXRXX240011_dorado7213sup_mm226.bam
    • BAM index: PNXRXX240011_dorado7213sup_mm226.bam.bai

ONT R10.4.1 4kHz chemistry - DNA data

NA24385 (HG002) PromethION data (~30X)

• Info: sheared DNA libraries (~17Kb) were prepared using the ONT LSK114 ligation library prep and a R10.4.1 flow cell at 4KHz sampling rate was used to generate ~30X genome coverage.
• Notes: the complete dataset with 15.3M reads (102.2 Gbases). Also available on SRA: SRS16575602.
• Reads lengths: 6.5 kbases median, 7.3 kbases mean, 636.6 kbases max
• Browse: https://gtgseq.s3.amazonaws.com/index.html#ont-r10-dna/NA24385/

raw signal data:

• BLOW5 file
  • direct link: PGXX22394_reads.blow5
  • s3 location: s3://gtgseq/ont-r10-dna/NA24385/raw/PGXX22394_reads.blow5
  • md5sum: 3498b595ac7c79a3d2dce47454095610
• BLOW5 index
  • direct link: PGXX22394_reads.blow5.idx
  • s3 location: s3://gtgseq/ont-r10-dna/NA24385/raw/PGXX22394_reads.blow5.idx
  • md5sum: 1e11735c10cf63edc4a7114f010cc472
• Also available on SRA: SRR23215366
• Also available on ENA: ERR11777845

basecalls:

• Guppy 6.4.2 high accuracy
  • basecalled with Guppy 6.4.2 through buttery-eel.
  • model: dna_r10.4.1_e8.2_400bps_hac_prom.cfg
  • only reads that passed the qscore filter threshold 9 are included
    • FASTQ: PGXX22394_guppy642hac.fastq.gz
    • FASTQ index: PGXX22394_guppy642hac.fastq.gz.gzi and PGXX22394_guppy642hac.fastq.gz.fai
  • mapped with minimap2 2.17 against hg38noAlt with map-ont preset
    • BAM: PGXX22394_guppy642hac_mm217.bam
    • BAM index: PGXX22394_guppy642hac_mm217.bam.bai

modcalls

• f5c 1.2 CpG methylation frequencies
  • PGXX22394_guppy642hac_mm217.bam and PGXX22394_guppy642hac.fastq.gz used as input
  • bgzip compressed methylation frequencies: PGXX22394_guppy642hac_mm217_f5c12_mfreq.tsv.gz

NA12878 (HG001) PromethION data (~20X)

• Info: Sheared DNA libraries (~30Kb) were prepared using the ONT LSK114 ligation library prep and a R10.4.1 flow cell at 4KHz sampling rate was used to generate ~30X genome coverage.
• Notes: the complete dataset with ~11M reads (70.5 Gbases)
• Reads lengths: 4.5 kbases median, 7.6 kbases mean, 235.1 kbases max
• Browse: https://gtgseq.s3.amazonaws.com/index.html#ont-r10-dna/NA12878/

raw signal data:

• BLOW5 file
  • direct link: PGXXHX230142_reads.blow5
  • s3 location: s3://gtgseq/ont-r10-dna/NA12878/raw/PGXXHX230142_reads.blow5
  • md5sum: 24266f6dabb8d679f7f520be6aa22694
• BLOW5 index
  • direct link: PGXXHX230142_reads.blow5.idx
  • s3 location: s3://gtgseq/ont-r10-dna/NA12878/raw/PGXXHX230142_reads.blow5.idx
  • md5sum: a5659f829b9410616391427b2526b853
• Also available on ENA: ERR11777844

basecalls:

• Guppy 6.4.2 high accuracy
  • basecalled with Guppy 6.4.2 through buttery-eel.
  • model: dna_r10.4.1_e8.2_400bps_hac_prom.cfg
  • only reads that passed the qscore filter threshold 9 are included
    • FASTQ: PGXXHX230142_guppy642hac.fastq.gz
    • FASTQ index: PGXXHX230142_guppy642hac.fastq.gz.gzi and PGXXHX230142_guppy642hac.fastq.gz.fai
  • mapped with minimap2 2.17 against hg38noAlt with map-ont preset
    • BAM: PGXXHX230142_guppy642hac_mm217.bam
    • BAM index: PGXXHX230142_guppy642hac_mm217.bam.bai

modcalls

• f5c 1.2 CpG methylation frequencies
  • PGXXHX230142_guppy642hac_mm217.bam and PGXXHX230142_guppy642hac.fastq.gz used as input
  • bgzip compressed methylation freqencies: PGXXHX230142_guppy642hac_mm217_f5c12_mfreq.tsv.gz

---

Please cite the following in your publications when using this dataset:

Bonson Wong, James M Ferguson, Jessica Y Do, Hasindu Gamaarachchi, Ira W Deveson, Streamlining remote nanopore data access with slow5curl, GigaScience, Volume 13, 2024, giae016, https://doi.org/10.1093/gigascience/giae016

@article{10.1093/gigascience/giae016,
    title="{Streamlining remote nanopore data access with slow5curl}",
    author={Wong, Bonson and Ferguson, James M and Do, Jessica Y and Gamaarachchi, Hasindu and Deveson, Ira W},
    journal={GigaScience},
    volume={13},
    pages={7},
    year={2024},
    publisher={Oxford University Press},
}