Overlap File for RACON Genome Polisher

Overlap File for RACON Genome Polisher

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This seems like a dumb question, but I have no idea how to generate an overlap file that is required for RACON. According to the documentation: github.com/isovic/racon

Racon takes as input only three files: contigs in FASTA/FASTQ format, reads in FASTA/FASTQ format and overlaps/alignments between the reads and the contigs in MHAP/PAF/SAM format. Output is a set of polished contigs in FASTA format printed to stdout. All input files can be compressed with gzip (which will have impact on parsing time).

I have PacBio CLR data, and I have Illumina PE data. I would like to use the illumina data to polish the pacbio data.

How do I generate the “overlap” file? If I use MHAP, I get a output file in <*.dat> format. How do I convert this into an MHAP format?


minimap2


overlap


racon


MHAP

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