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lh3 / minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences
https://lh3.github.io/minimap2
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general question about supplementary alignments #1216

Closed alisamatisse closed 3 months ago

alisamatisse commented 3 months ago

Hello, sorry for this question, but how is supplementary alignment determined (the algorithm)? I know it is chimeric reads, but I was really surprised to have 60% of chimeric reads in my samples after MDA 🤔 Also, I checked some publicly available datasets and was surprised to see that even without MDA there are 4.5-12% reads having SA flag (PacBio, ONT). Isn't it too much structural variation to expect.. ?

lh3 commented 3 months ago

If minimap2 can't find an end-to-end alignment, it will generate chimeric alignment. MDA is known to have such artifacts. PTA is better.

alisamatisse commented 3 months ago

thanks!