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GSTT-CIDR / influenza_r9.4.1_rbk_2022

In-house python scripts for influenza virus sequencing using Nanopore, made available to accompany https://doi.org/MGEN-D-23-00116
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IRMA configuration #1

Closed Albertperlas closed 1 week ago

Albertperlas commented 1 year ago

Hi,

I would like to ask you about your IRMA configuration: FLU-minion-final. Can you specify a bit more about this? How have you modified the FLU-minion configuration?

Thanks, Albert Perlas

TGSWilliams commented 1 week ago

Hi,

This is detailed in the supplementary methods:

“Consensus generation and control analysis The FLU-minion config file was adapted as follows: the MIN_CONS_SUPPORT parameter was set to 20 to provide a consensus base call with a read depth of 20, MIN_AMBIG set to 0.5 to prevent mixed base calls, and ASSEM_PROG set to MINIMAP2.”

Thanks