General Settings

ONT Dir. (Required)

Set the path to the Nanopore reads directory.

Note

• Example: /path/to/your/ONT/reads/directory

Illumina Dir. (Optional/Required)

Set the path to the Illumina reads directory.

Note

• Example: /path/to/your/Illumina/reads/directory
• Required if “hybrid-assembly” or/and “polishing” is/are used.

Warning

• If the structure of Illumina reads filename is Prefix_{1,2}.fastq.gz (for example: ID40_1.fastq.gz, ID40_2.fastq), these Illumina reads will be trimmed.
• If the structure of Illumina reads filename is Prefix_HQ_{1,2}.fastq.gz (for example: ID40_HQ_1.fastq.gz, ID40_HQ_2.fastq), these Illumina reads will not be trimmed.

Output Dir. (Required)

Set the path to the output directory.

Note

• Example: /path/to/your/output/directory

Sample sheet (Optional)

Set the path to the sample sheet file.

Note

• The sample sheet file type must be CSV or TSV.

Warning

• Underscore(‘_’) is not allowed in the sample name.

Prefix (Optional)

Set the prefix for the Nanopore reads after demultiplexing.

Note

• Example: ID .
• Default: barcode .

Threads (Required)

Set the number of threads/cpus to run the analysis.

Note

• Default: 8.

Barcodes (Optional)

Set which barcodes will be analyzed. Put in the numbers and separate them with a comma.

Note

• Example: 1,2,3,4
• If you want to analysis all barcodes, leave it blank.