cornetto

Data used in the preprint/publication

FASTQ and BLOW5

The ENA project PRJEB86853 contains raw data with file name prefixes as in this tsv file here. In the tsv table:

• For PacBio HiFi data there should be one fastq.gz file.
• For ONT data there should ba a fastq.gz containing basecalled reads and a tar.gz containing raw signal BLOW5 files.
• Note that FASTQ files contain what was given to the assembler, that are already filtered (e.g., pass reads, qscore cut off).
• FASTQ for ONT duplex samples only contain duplex reads.
• For cornetto rounds for ONT simplex, FASTQ files contain reads >30kbase.
• BLOW5 files contain everything that came out of the sequencing run without any filtering.
• Those with T2TC inside brackets are where we used publicly available data from T2T Consortium’s human pangenomics AWS bucket. The links we used are:
  • m84005_220827_014912_s1 (T2TC)
  • HG002_3 (T2TC), HG002_6 (T2TC), HG002_2 (T2TC), HG002_9 (T2TC), HG002_4 (T2TC), HG002_8 (T2TC)
• *hg002-Cornetto-x.1 is made of fastq0+fastq1; hg002-Cornetto-x.2 is made of fastq0+fastq1+fastq2; and so on.

FASTA assembly

HG002

The files in the table here are found inside the cornetto-hg002-asm directory created when you download and extract the cornetto-hg002-asm.tar.gz file from https://doi.org/10.5061/dryad.kkwh70sfr.

Note: ‘hg002-Cornetto-4.3 (final)’ is only applicable for the first version of the manuscript preprint. For the updated assemblies used in the updated version of the manuscript preprint (and the published paper), please see the HG002-updates section below.

Animals

The files in the table here are found inside the cornetto-animal-asm directory created when you download and extract the cornetto-animal-asm.tar.gz file from https://doi.org/10.5061/dryad.kkwh70sfr

HG002-updates

The files in the table here are found inside the cornetto-hg002-asm-updates directory created when you download and extract the cornetto-hg002-asm-updates.tar.gz file from https://doi.org/10.5061/dryad.kkwh70sfr.

This contains the updated ‘hg002-Cornetto-4.3’ assemblies created during the manuscript revision. This also includes a copy of the ‘T2TC-ONT’ assemblies used for comparison.

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