Input File Structure

Start from Base Calling

Start the pipeline from Base calling.

ONT_Reads_Directory/
├── HPz800_20180821_FAJ18422_MN17776_sequencing_run_VIM4_Janina_26844_read_11_ch_171_strand.fast5
├── HPz800_20180821_FAJ18422_MN17776_sequencing_run_VIM4_Janina_26844_read_11_ch_203_strand.fast5
├── HPz800_20180821_FAJ18422_MN17776_sequencing_run_VIM4_Janina_26844_read_15_ch_344_strand.fast5
├── HPz800_20180821_FAJ18422_MN17776_sequencing_run_VIM4_Janina_26844_read_17_ch_249_strand.fast5
├── HPz800_20180821_FAJ18422_MN17776_sequencing_run_VIM4_Janina_26844_read_19_ch_397_strand.fast5
└── ......

Illumina_Reads_Directory/
├── Prefix01_HQ_1.fastq.gz
├── Prefix01_HQ_2.fastq.gz
├── Prefix02_HQ_1.fastq.gz
├── Prefix02_HQ_2.fastq.gz
├── Prefix03_HQ_1.fastq.gz
├── Prefix03_HQ_2.fastq.gz
└── ......

Note

• Illumina reads files naming structure for each pair: Prefix_HQ_1.fastq.gz Prefix_HQ_2.fastq.gz
• If there is without “HQ” in the file name, these Illumina reads will be trimmed.
• “Prefix” is the sample name, each pair should has its own prefix.
• “*” means arbitrarily long characters.

Warning

• Do not use underscore (“_”) in the prefix.

Start from Demultiplexing

Start the pipeline from Demultiplexing.

ONT_Reads_Directory/
├── fastq_runid_50a6171cadcfb6b5cb2dae4e75a0ccc05b71e3d8_0.fastq
├── fastq_runid_50a6171cadcfb6b5cb2dae4e75a0ccc05b71e3d8_1.fastq
├── fastq_runid_50a6171cadcfb6b5cb2dae4e75a0ccc05b71e3d8_2.fastq
├── fastq_runid_50a6171cadcfb6b5cb2dae4e75a0ccc05b71e3d8_3.fastq
├── fastq_runid_50a6171cadcfb6b5cb2dae4e75a0ccc05b71e3d8_4.fastq
└── ......

Illumina_Reads_Directory/
├── Prefix01_HQ_1.fastq.gz
├── Prefix01_HQ_2.fastq.gz
├── Prefix02_HQ_1.fastq.gz
├── Prefix02_HQ_2.fastq.gz
├── Prefix03_HQ_1.fastq.gz
├── Prefix03_HQ_2.fastq.gz
└── ......

Start from Reads Filter

Start the pipeline from Reads Filter.

ONT_Reads_Directory/
├── Prefix01.fastq
├── Prefix02.fastq
├── Prefix03.fastq
├── Prefix04.fastq
├── Prefix05.fastq
└── ......

Illumina_Reads_Directory/
├── Prefix01_HQ_1.fastq.gz
├── Prefix01_HQ_2.fastq.gz
├── Prefix02_HQ_1.fastq.gz
├── Prefix02_HQ_2.fastq.gz
├── Prefix03_HQ_1.fastq.gz
├── Prefix03_HQ_2.fastq.gz
└── ......

Start from Assembly

Start the pipeline from Assembly.

ONT_Reads_Directory/
├── Prefix01.fastq
├── Prefix02.fastq
├── Prefix03.fastq
├── Prefix04.fastq
├── Prefix05.fastq
└── ......

Illumina_Reads_Directory/
├── Prefix01_HQ_1.fastq.gz
├── Prefix01_HQ_2.fastq.gz
├── Prefix02_HQ_1.fastq.gz
├── Prefix02_HQ_2.fastq.gz
├── Prefix03_HQ_1.fastq.gz
├── Prefix03_HQ_2.fastq.gz
└── ......

Start from Polishing

Start the pipeline from Polishing.

ONT_Reads_Directory/
├── Prefix01.fasta
├── Prefix02.fasta
├── Prefix03.fasta
├── Prefix04.fasta
├── Prefix05.fasta
└── ......

Illumina_Reads_Directory/
├── Prefix01_HQ_1.fastq.gz
├── Prefix01_HQ_2.fastq.gz
├── Prefix02_HQ_1.fastq.gz
├── Prefix02_HQ_2.fastq.gz
├── Prefix03_HQ_1.fastq.gz
├── Prefix03_HQ_2.fastq.gz
└── ......

Sample Sheet

Sample Sheet

Sample	Barcode
example1	barcode01
example2	barcode02
example3	barcode03
example4	barcode04
example5	barcode05

Note

• The type of sample sheet file is CSV (split cell contents by comma) or TSV (split cell contents by tab).
• The format of barcode name: barcodeXX (“barcode” can be any characters, but XX must be two digits: 01,02,03,…,10,11,12,…)