Closed RolandFaure closed 3 months ago
Hi, You are correct. There is unfortunately a side effect of windowing, if the window boundary happens to fall on an indel region.
There are a couple of options you may try:
Hope this helps, Best regards, Ivan.
Hello,
Thanks for developping Racon, I use it all the time :smiley:
I am polishing amplicon sequences (they are short, usually less than 1000bp), and I noticed that racon sometimes introduced small indels at position 500 of the consensus, which I suppose is linked with the fact that 500 is the size of the default window. Do you know where this issue might come from ?
Attached is one very small example: racon_pb.gz
I have v1.4.20 and here is the command lines used:
Around position 500 of polished_0.fasta I obtain the sequence "TGTGCAGATTTTTGACAA", which is in none of the reads and should instead be "TGTGTGCGATTTTTGACAA".
Thanks in advance