Minimap2: Soft-clipping at contig ends

[Adamtaranto]

Hi Heng Li,

I'm trying to find long-reads whose primary alignment overhangs the end of a contig, and that might provide useful information to extend the contig or bridge two split contigs. I see that mm2 supports soft clipping in supplementary alignments, but I am wondering how it will handle reads where the best match potentially has a large fraction of its length dangling off a contig end?

Are there any other settings that you would advise tweaking to help recover these kinds of reads?

Thanks for your help.

[lh3]

how it will handle reads where the best match potentially has a large fraction of its length dangling off a contig end?

That is just soft clip.

[tseemann]

@Adamtaranto samclip might be useful for you (maybe)
https://github.com/tseemann/samclip

[Adamtaranto]

Thanks, @tseemann ! I'll give it a try.

[Adamtaranto]

Update: In case anyone needs to fish out Minimap2 alignments that are soft-clipped at contig ends, I've written a tool called Teloclip to do just that.

It also includes an option to test reads for telomeric repeat motifs.

[tseemann]

That README.md looks very familiar @Adamtaranto :-P