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Check compatibility with Nanopore #301

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Emkago opened this issue May 17, 2024 · 2 comments
Open

Check compatibility with Nanopore #301

Emkago opened this issue May 17, 2024 · 2 comments
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@Emkago
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Emkago commented May 17, 2024

Review existing tools in the pipeline if they can take in Nanopore data. If not, find a suitable alternative for long reads.

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Emkago commented May 27, 2024

Checking tool compatibility for MRSA workflow: all of the existing tools for identification of virulence genes and typing could be used with Nanopore data (excluding Freebayes). Others often use Prokka in addition for detection of gene norA.

@ryanjameskennedy ryanjameskennedy added the high High priority label Jan 9, 2025
@ryanjameskennedy ryanjameskennedy added this to the Nanopore milestone Jan 20, 2025
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Emkago commented Jan 23, 2025

Turn off fastqc module for Nanopore data. NanoPlot was implemented for this purpose.

Turn off bwa module and postalignqc , add minimap2 to map reads to a reference as a part of QC.

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