Completed on 16 Apr 2016 by Torsten Seemann . Sourced from http://biorxiv.org/content/early/2016/04/17/048942.
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Author response is in blue.
I think this tool does home potential to improve plasmid assembly and recovery.
I have some comments:
(1) I feel it is overstating the problem of plasmids being missed. They are usually in the contigs (and graph) but obviously fragmented and sometimes joined to the chromosome graph, but they are there, and can be baited by looking for classical plasmid genes (rep etc).
(2) The text has no actual description of the algorithm method, or any structured results.
(3) The code/binary uses the same exe names etc as regular Spades, so it is difficult to install alongside regular spades.
(4) It seemed to ignore my --threads parameter (at least for hammer stage)
(5) I fed it a challenging multi plasmid data set of GAI data (PE 36 bp) and it failed on "-k auto" because it said k=55 was bigger than read length. I assumed "-k auto" would know the readlength as it just indexed/corrected all the reads?
I look forward to further development of plasmidSpades and the integration of the methods into regular Spades.
Thank you for feedback!
1) Thank you, this is reasonable consideration to add.
2) There was some mess about conference online proceedings and restrictions on journal submission . We've uploaded a full version of the draft.
3) We plan to include plasmidSPAdes as an option into next SPAdes release.
4-5) Some parts of hammer are not run in parallel, However, thanks for the report, will check this issues before next release.