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artic-network / fieldbioinformatics

The ARTIC field bioinformatics pipeline
MIT License
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Streamline nanopolish indexing #6

Closed jts closed 4 years ago

jts commented 4 years ago

artic gather now builds nanopolish index files for the full read set, using the summary files it detects artic demultiplex will build an index for barcoded fastqs, using the master .readdb file to avoid lengthy re-indexing

This improves the pipeline by reducing some steps (nanopolish index does not need to be run separately) and removes the need to pass nanopolish-reads-file to artic minion.