Tool:Workflow for structural variants from long read sequencing data

Question

[WouterDeCoster]

We (pluralis maiestatis) have developed a worfklow/pipeline to identify, annotate and visualize structural variation from long read sequencing data (Oxford Nanopore and PacBio).

This is based on Snakemake and can be found on GitHub: https://github.com/wdecoster/nano-snakemake

Integrated are recently developed aligners (minimap2 and ngmlr) and specific variant callers (sniffles, nanosv and npInv). More information about this can also be found in our preprint on structural variants in NA19240 PromethION data.

All feedback and contributions are welcome!

[BioinformaticsLad]

I'd like to try to out this pipeline. I checked the github but couldn't find a user manual or wiki.

[WouterDeCoster]

The pipeline uses Snakemake, so I would suggest you familiarize yourself with using that. Please open an issue on GitHub with a more specific question if you can't get this to work.

[BioinformaticsLad]

Great, I'll check it out. So everything has been pre-configured to run without messing with any options or parameters I assume.

[Picasa]

Hi,

Do you recommend to use corrected pacbio reads (with canu for instance) or raw pacbio reads ?

[WouterDeCoster]

Raw would be good. Coverage is more important than nucleotide accuracy.

[Kumar]

Does this pipeline work with genomic data of trees?

[WouterDeCoster]

Sure, just don't forget to set the appropriate reference genome.