This page contains conveinence links to data used for the verkko manuscript as well as all assemblies from the paper.

Source code:

• verkko beta2
• rukki tagged
• graphaligner 1.0.15
• mbg 1.0.9

The archived code is also available at zenodo.

Data links

• A. thaliana:

  • https://ngdc.cncb.ac.cn/bioproject/browse/PRJCA005809

• H. axyridis:

  • https://www.ebi.ac.uk/ena/browser/view/PRJEB45202?show=component-projects
  • https://raw.githubusercontent.com/darwintreeoflife/darwintreeoflife.data/master/species/Harmonia_axyridis/Harmonia_axyridis.md

• CHM13 (HiFi data and the rel5 ONT dataset):

  • https://github.com/marbl/CHM13

• HG002:

  • https://s3-us-west-2.amazonaws.com/human-pangenomics/index.html?prefix=

  • HG002 Hi-C:

    • https://s3-us-west-2.amazonaws.com/human-pangenomics/index.html?prefix=NHGRI_UCSC_panel/HG002/hpp_HG002_NA24385_son_v1/hic/downsampled/*NovaSeq*.

  • HG002 35x HiFi:

    • https://s3-us-west-2.amazonaws.com/human-pangenomics/index.html?prefix=NHGRI_UCSC_panel/HG002/hpp_HG002_NA24385_son_v1/PacBio_HiFi/downsampled/

  • HG002 35x DeepConsensus HiFi:

    • https://storage.googleapis.com/brain-genomics/awcarroll/t2t/fastq/q20/m64011_190830_220126.Q20.fastq.gz
    • https://storage.googleapis.com/brain-genomics/awcarroll/t2t/fastq/q20/m64011_190901_095311.Q20.fastq.gz
    • https://storage.googleapis.com/brain-genomics/awcarroll/t2t/fastq/q20/m64012_190920_173625.Q20.fastq.gz
    • https://storage.googleapis.com/brain-genomics/awcarroll/t2t/fastq/q20/m64012_190921_234837.Q20.fastq.gz

  • HG002 60x ONT UL:

    • https://s3-us-west-2.amazonaws.com/human-pangenomics/index.html?prefix=NHGRI_UCSC_panel/HG002/hpp_HG002_NA24385_son_v1/nanopore/downsampled/greater_than_100kb/

  • HG002 105x HiFi:

    • https://s3-us-west-2.amazonaws.com/human-pangenomics/index.html?prefix=
      • m54329U_201103_231616.ccs.fastq.gz
      • m64004_210224_230828.hifi_reads.fastq.gz
      • m64011_190830_220126.Q20.fastq.gz
      • m64011_190901_095311.Q20.fastq.gz
      • m64012_190920_173625.fastq.gz
      • m64012_190921_234837.fastq.gz
      • m64014_210227_165255.hifi_reads.fastq.gz
      • m64015e_210223_010616.hifi_reads.fastq.gz
      • m64015e_210224_100310.hifi_reads.fastq.gz
      • m64076_201013_225902.ccs.fastq.gz
      • m64076_201016_191536.ccs.fastq.gz
      • m64076_210310_104300.hifi_reads.fastq.gz

  • HG002 85x ONT UL:

    • https://s3-us-west-2.amazonaws.com/human-pangenomics/index.html?prefix=NHGRI_UCSC_panel/HG002/nanopore/Guppy_4.2.2/
    • s3://ont-open-data/gm24385_2020.11/analysis/r9.4.1/20201026_1644_2-E5-H5_PAG07162_d7f262d5/guppy_v4.0.11_r9.4.1_hac_prom/basecalls.fastq.gz
    • s3://ont-open-data/gm24385_2020.11/analysis/r9.4.1/20201026_1645_6B_PAG07165_d42912aa/guppy_v4.0.11_r9.4.1_hac_prom/basecalls.fastq.gz
    • s3://ont-open-data/gm24385_2020.11/analysis/r9.4.1/20201102_1746_6C_PAG07506_acad8a68/guppy_v4.0.11_r9.4.1_hac_prom/basecalls.fastq.gz

  • HG002 Father:

    • https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/HG003_NA24149_father/NIST_Illumina_2x250bps/reads/

  • HG002 Mother:

    • https://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/AshkenazimTrio/HG004_NA24143_mother/NIST_Illumina_2x250bps/reads/

  • HG002 pre-built parental hapmers (k=30, homopolymer compressed):

    • https://s3-us-west-2.amazonaws.com/human-pangenomics/index.html?prefix=T2T/HG002/qc/

Assemblies

The archive of results is also available at zenodo