Here is my problem. I have a reference file with all 32-mers found in the human transcriptome. I would have a search file of 32-mers from short read sequencing data. I would like to determine if any of the 32-mers in the search file are present in the reference file. The search should be of the approximate k-mer search type, as I expect the 32-mers from sequence data to have errors and in some cases variants. Do you know of a tool that can solve my problem? Thank you
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written
by
Anjan
2 answers
Since you've already got both ref and query k-mers sets, you can only use technologies such as simhash which support approximate k-mer match.
ref
Are you looking for a tool or a library? I think this paper and some of the references would be a good start for the fundamentals, and HyperGen looks like a fancy new library. As a ready to use tool, Sylph may be what you are looking for - but you need to provide Fasta/FastQ input and not precomputed k-mers.
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