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mrmckain / Fast-Plast

Automated de novo assembly of whole chloroplast genomes.
MIT License
43 stars 14 forks source link

Using user_bowtie #35

Closed nsmt89 closed 5 years ago

nsmt89 commented 5 years ago

Hi, I am trying to assemble chloroplast from my raw WGS data. I would like to use my own reference genome, how can I use it as user_bowtie?

mrmckain commented 5 years ago

You need to create the Bowtie2 indices yourself and give then path for them with the --user_bowtie option.

Best, Michael