animal_mt

[yergol]

Hi,

I want to use GetOrganelle for assembly of animal mitochondrial genome with Illumina reads. The reads were polished with a pipeline including trimming and merging. The polished reads are composed of merged forward and reverse reads and unpaired read files. I was confused about which data I should continue with for GetOrganelle run and which mode -paired end or single end- I should use for unpaired data. If possible, I would like to hear your suggestions.

Thank you so much!

[JianjunJin]

Please find a short instruction here. Basically, we do not recommend reads polishing. We also do not have options for merged paired-end reads.

-1 and -2 are for paired-end reads, while -u is for unpaired reads (multiple files split with commas).