Circularized genome output file missing!

[ghost]

Good day Nick, Thanks for updating and maintaining the repository. Wish you a fruitful 2019. One of many mitogenome assembly runs on an Antarctic insect species ends with producing a full 15K mitogenome and another 5K long contig. The 15k output is not actually circularized. Is it because there are two contigs or it might be an another issue with 15k long contig? Do you recommend any external tool for circularizing the long contig? Thanks in advance Arsalan

[ndierckx]

I could be a repetitive control region, which are very hard to assemble with short reads. Have you checked if the second contig is repetitive?

[ghost]

Thanks Nick, It seems that your suspicion is correct. When I use another "relatively closely related species" as reference to help resolving repeats, the end of the assembly is something like the sequence I have embedded below. The small contig disappeared totally.However the 15K assembly is still not circularized. I appreciate your kind advice. I can send you log files incase needed. Cheers

TTTTACTTACTGAAATGTAGTAGCCAGTTTAGGTTCTATTGTGTCTGTGATTTCTGTYATATTTTTTTTATTTATTATTTGAGAAGCTTTTGTCAGGCATCGGCCAGCTTTGTCGAGGAATCACTTGTCTTCTTCTTTGGAAATAATACACTCGTTCCCGCCGTTAAACCATAGATATTCTTCTATTCCCGTTATTAGAAATAAGTTATATATAAGTGTTTTGCATTAGAAATTTTGATTTTCTAGGACGTAATTAAAAATTATGATATATAGCGAGTATACTTACCTTATTTATTGGTTACTGACTTCYTGAGAGAGAAAAAAAAAAGMAAMCAAGTTTACTTCAGTAGTTTTAAAWTTTTGATTACGAAATTATTATTTTTTTGCTATTTTATTAATAGTCTAGCGWGTGGGGGGGGGGGGGGGGGGG

[ndierckx]

For repetitive control regions, it's no point in giving a reference, there is to much variation, even between individuals of the same species. Run it again without the reference with extended log option to 1 and send me that log and the merged file, I will check if it is possible to circularize

[ghost]

Thanks Nick! It is very kind of you. Please find attached the file that you requested. Highly appreciate your kind time.

config.txt Contigs_1_copepod_noref.fasta.txt log_extended_copepod_noref.txt