First, thank you for making this workflow available, it is very helpful! Despite being new to these assemblers, I have been able to quickly assemble mitogenomes with MitoComp and sort out genes of interest (e.g. COI) from metagenomes.
Your workflow has worked well for most of my files, but for some samples I am getting error messages and I am not sure how to resolve these cases. For example, the error message "Empty blast frame!" recommends that I check data quality. I can see that after quality trimming, most reads are kept for downstream steps in the analysis. I was wondering if you would have any advice for finding out what is causing mitoflex to be unable to assemble these samples.
First, thank you for making this workflow available, it is very helpful! Despite being new to these assemblers, I have been able to quickly assemble mitogenomes with MitoComp and sort out genes of interest (e.g. COI) from metagenomes.
Your workflow has worked well for most of my files, but for some samples I am getting error messages and I am not sure how to resolve these cases. For example, the error message "Empty blast frame!" recommends that I check data quality. I can see that after quality trimming, most reads are kept for downstream steps in the analysis. I was wondering if you would have any advice for finding out what is causing mitoflex to be unable to assemble these samples.