Minimap2 Output

Question

[Jon]

I'm trying to understand Minimap2 output. The mapped reads include paired reads (interlaced), with singletons mixed within these results. I'm trying to understand this, and how to use the output. Can I use these reads directly into Metaspades, paired with singletons??

I'm guessing that what I'm seeing are what it classifies as a chimeric sequence, where only one strand matches, so the mapped reads will include single end where only one read matches the reference, and other other goes as a single read as unmapped??

Answer 1

[Istvan Albert]

Minimap 2 has two outputs the PAF format and the SAM format.

Each has a documentation that describes how the information is encoded. In general paried-end input will generate paired-end output. Supplementary alignments (chimeric) alignments typically refer to situations where complementary regions of the SAME read align to different,potentially distant regions in the genome.