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SouthGreenPlatform / culebrONT

A snakemake pipeline to assembly, polishing, correction and quality check from Oxford nanopore reads.
GNU General Public License v3.0
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run PacBio data without REF and FAST5 #10

Closed yangzuokun closed 1 year ago

yangzuokun commented 1 year ago

Hi I'm trying to run PacBio data, but no REF and FAST5 files, how to prepare these?

francoissabot commented 1 year ago

You do not need FAST5 (raw Nanopore data) or reference to run a simple assembly. Just do not activate Medaka (dedicated to Nanopore anyway) and comparison to reference.

yangzuokun commented 1 year ago

![image](https://user-images.githubusercontent.com/33180540/202824812-d01b3890-64b5-409e-8563-c1e5fe02ed52.png

yangzuokun commented 1 year ago

But how to define the REF and FAST5 in config.yaml ?

sravel commented 1 year ago

Hello, you can let emtpy string value like this

DATA:
    FASTQ: '/path/to/fastq/directory/'
    REF: ''
    GENOME_SIZE: '1m'
    FAST5: ''
    ILLUMINA: '/path/to/illumina/directory/'
    OUTPUT: '/path/to/output/directory/'