Request for dataset to test --ont functionality

[SaimMomin12]

Hi, I would like to test the new functionality of --ont and subsequently integrate it into Galaxy for our users.

Assemble genomes with ONT R10 reads rather than PacBio HiFi reads using the latest release of hifiasm (>0.21.0-r686)
hifiasm -o HG002.asm --ont -t32 HG002-ont.fq.gz

Could you please point me to a dataset that can be used to test this option?

Thank you!

[chhylp123]

Please have a try for 0.24.0 currently and we will also release a new version soon. The latest version will often give you better results.

You can find three R10 datasets (HG002_R10, HG00733_R10, and HG02723_R10) at: https://s3-us-west-2.amazonaws.com/human-pangenomics/index.html?prefix=publications/Napu_paper_ONT_Coriell_SingleFC_2023/. Data come from https://github.com/nanoporegenomics/napu_wf.

[SaimMomin12]

@chhylp123 Thanks for the super prompt reply and for sharing the link!

I looked into the HG002_R10 directory but couldn't find the FASTQ files required for running hifiasm --ont mode. Am I missing something, or are the FASTQ files located elsewhere?

Thanks in advance for your help!

[chhylp123]

The reads are in bam format. For example, HG002 reads can be found: /HG002_R10/reads/GM24385_R10_638.bam. You will need samtools fastq to convert it into fastq format for hifiasm.

[SaimMomin12]

Thanks for the clarification. However, the dataset seems quite large in terms of storage.

Would it be possible to provide a smaller toy dataset for testing the --ont functionality? That would help in quickly validating and further adding it to Galaxy.

[chhylp123]

You can align HG002 reads back to grch38. And then extract reads within that region using samtools. This subset of reads will work for hifiasm (ONT).

[chhylp123]

Sorry I forget to mention the coordinate. We often use chr11:10M-20M for test.

[SaimMomin12]

Thanks for the suggestion, I will try out!