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lh3 / minigraph

Sequence-to-graph mapper and graph generator
https://lh3.github.io/minigraph
MIT License
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multiple mapping #107

Closed yjk-bertrand closed 10 months ago

yjk-bertrand commented 10 months ago

I am using a blunted assembly graph from short reads that contains several paralogs. I am aligning a long read to the graph that should partially match several paths on the graph. I have tried several combinations of mapping parameters, varying the sequence divergence, the number of secondary alignments and other attempts. Yet, minigraph always outputs a single mapping for the query. Is there a way to get every mapping, even the partial ones?

lh3 commented 10 months ago

Minigraph may map a read to different loci with option --secondary=yes, but it can't map a read to different haplotypes at the same locus.