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niemasd / ViReflow

An elastically-scaling automated AWS pipeline for viral consensus sequence generation
GNU General Public License v3.0
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Add genome assembly as optional step #8

Closed niemasd closed 3 years ago

niemasd commented 3 years ago

It would be good to add genome assembly as an optional step, as it would be reasonably simple to add (it just depends on the trimmed BAM) and it would be able to run in parallel to the other steps of the pipeline

SPAdes would be a good option, as it has newly-added viral assembly features: https://cab.spbu.ru/software/spades/

niemasd commented 3 years ago

Added in ViReflow v1.0.11