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lh3 / miniasm

Ultrafast de novo assembly for long noisy reads (though having no consensus step)
MIT License
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Assemble of DNA and RNA amplicons from PacBio run #92

Closed s-t-calus closed 1 year ago

s-t-calus commented 1 year ago

I am trying to combine data from two PacBio runs: DNA (10kb) + cDNA (10kb), these regions overlap each other partially and I would like to phase them based on short-tandem repeats and exonic SNP/fingerprint to genomic exon+intron SNP fingerprints to identify intronic SNP and a number of tandem repeats that are separated by >150kb from each other. cDNA was used to bring STR's + exonic SNP closer to each other.

Do you think miniasm could assemble DNA (intronic and exonic) + RNA/cDNA reads (exonic) into a graph where we could: phase the number of STR's + exonic SNP (cDNA) with intronic and exonic fingerprints (DNA) based on 99-100% similarity?

If yes, which of the packages I should use, if not do you have any idea what software I should consider using e.g. UCLUST or VSEARCH for OTU binning?

lh3 commented 1 year ago

Miniasm is not intended for amplicons.