Closed josiah-liew closed 8 months ago
Sorry, dropped this completely. Looks like it could be part of a barcode/primer that was not removed?
You can specify the parameter --primer_file [FILE]
where FILE is a fasta file with custom primers that are removed after polishing.
HTH, Kristoffer
Hi Kristoffer. Thank you! We definitely did specify the --primer_files
. Something we've noticed is that the having too large a --s
produces the following but adjusting the --s
down removes the repeating sequences.
Thank you, Josiah
Hello, thank you for creating this tool.
I wanted to ask if you could provide any ideas as to the presence of the following repeating sequences (highlighted here). Recently, we've noticed that the blast output has a low % coverage. Looking deeper we've begun to notice sections in the consensus that seem to repeat itself at the 5'/3' ends and are not part of the identified organisms in blast. Manually removing these repeats (and some additionally bases) significantly improves both query and identity.