Long read filtering based on reference

Question

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Hi everyone!!

I'm diving into the world of long read sequencing. I want to do some quality filtering of my reads using Filtlong. According to the author filtering using a reference is a better way to go in comparison to quality parameter based filtering. I understand the reasoning behind it but my question is the following:

If I pick a reference from RefSeq and use the short reads as a filtering guide, does that mean that anything not present in this ref will be filtered out (plasmids for example)?

Thanks!

[GenoMax]

If I pick a reference from RefSeq and use the short reads as a filtering guide

Not quite sure what you are referring to? Are you looking to filter short read data against a reference? If may be better to use bbduk.sh from BBMap suite in filter mode or use seal.sh to bin the reads.

The tool you linked is meant for long reads (kb long) and may not work if you have short read data.