Long read support?

[Kirk3gaard]

Hi

Any plans to expand snippy with support for pacbio and nanopore reads? Noticed this tutorial demonstrating the cool stuff snippy can do https://training.galaxyproject.org/training-material/topics/variant-analysis/tutorials/microbial-variants/tutorial.html and came here to check it out. However, I could not find any mention of long reads.

Best regards Rasmus

[mcrone]

It's possible to just use the contigs option with a consensus fasta. That's what I have done with pacbio data. Obviously not useful with raw reads, but you can use pbaa to get the clusters.

[andersgs]

Thank you for your interest in Snippy. At the moment, our focus is all On our SARS-CoV-2 response.

A future version of Snippy will most likely include support for long reads. Unfortunately, no commitments at this point as to when that might happen.

[fconstancias]

Hi all, Any update regarding this? I will explore the approach suggested by @mcrone @Kirk3gaard, did you find an alternative tool to achieve detection of snps or indels using nanopore reads? Thanks

[crarlus]

One workaround would be to map the long reads with a suitable mapper (e.g. minimap2) and then use the --bam input option in snippy. Have not tried it so far but plan to implement it in snippySnake which wraps snippy.

Not sure though whether freebayes can model the nanopore errors well and whether variants between Illumina and ONT agree.

[Nilad]

Hi, re-up this thread. I am looking to compare snippy outputs between illumina and nanopore or pacbio data.

[JoshuaIszatt]

Very interested in a version of snippy that can map ONT reads to a genome. ^^^ Any news?