Quick question
r4carson opened this issue · 2 comments
r4carson commented
- pharokka version:
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Description
I was just wondering if the meta -m flag assemble a phage genome or should I assemble the genome first? Does meta -m flag only combine contigs from the consensus sequence?
gbouras13 commented
Hi @r4carson,
Thanks for the great question!
Pharokka does not do assembly at all, nor does it combine contigs. All -m does is tell pharokka to expect multiple contigs in the input file, so it can do some things in the background to make it run a lot faster. If you have multiple contigs from a metagenome, definitely use -m, otherwise don’t.
For assembly I’d recommend metaspades, megahit or flye depending on your reads. For the combining of assemblies I’d recommend phables https://github.com/Vini2/phables.
George