Automatically extend contigs

[ihbxiongjie]

Hi, I am wondering is there any way (not the manual checking) to extend the contigs according to the telomere overhangs identified?

Thx

[Adamtaranto]

There is a secondary tool packaged with teloclip called teloclip-extract, this tool will output all the overhangs for each end of each contig.

The overhanging region of each read is in lowercase in the output files. You can selected the longest overhang and manually append it to the relevant contig.

Alternatively, you can assemble all the overhanging reads with miniasm which should give a single contig if all reads were correctly mapped and then re-process this new contig with teloclip-extract to get a single overhang segment with which to extend your contig.

Remember to polish your extended contigs with long-read (Racon) and/or short-read (Pilon) polishers.

I might automate the process later but it will always be best to manually inspect the alignments to avoid introducing errors