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GRIDSS: the Genomic Rearrangement IDentification Software Suite
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gridss for long-read data? #636

Closed kerstinth closed 1 year ago

kerstinth commented 1 year ago

Hi,

Out of curiosity - do you have any experience in running GRIDSS on long-read sequencing data? Or do you have any thoughts on whether this would work?

Best wishes, Kerstin

d-cameron commented 1 year ago

Gridss does not support long read data. This is due to a) the Gridss assembler assuming an illumina-like error model and not handling indel errors; b) the use of bwa mem for split read & assembly alignment (not a critical blocker as the aligner can be swapped out for a different one); and c) memory usage optimised for short reads (so Mb length ONT reads would cause a large % of the input bam to be loaded and cause out of memory errors.

It might work with error-corrected pacbio hifi reads but I don't expect it to outperform a proper long read sv caller such as sniffles.

On Tue, 8 Aug 2023, 2:03 am kerstinth, @.***> wrote:

Hi,

Out of curiosity - do you have any experience in running GRIDSS on long-read sequencing data? Or do you have any thoughts on whether this would work?

Best wishes, Kerstin

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kerstinth commented 1 year ago

Thanks very much for explaining this - that's great to know!