De novo Assembly of Illumina PE and Nanopore Reads
The workflow sample described below takes FASTQ files with paired-end Illumina reads and FASTQ file(s) with Oxford Nanopore reads and assembles these data de novo using SPAdes.
How to Use This Sample
If you haven’t used the workflow samples in UGENE before, refer to the “How to Use Sample Workflows” section of the documentation.
Workflow Sample Location
The workflow sample “De novo Assembly of Illumina PE and Nanopore Reads” can be found in the “NGS” section of the Workflow Designer samples.
Workflow Image
The opened workflow looks as follows:
Workflow Wizard
The wizard has four pages.
1. Input Data: Illumina Reads
On this page, you must set files with Illumina reads.
2. Input Data: Nanopore Reads
You must set the Nanopore reads on this page.
3. SPAdes Settings
You can change the default SPAdes parameters here.
The following parameters are available:
| Parameter | Description |
|---|---|
| Dataset type | Select the input dataset type: - Standard isolate (default) - Multiple displacement amplification ( --sc) |
| Running mode | By default, SPAdes performs both read error correction and assembly. You can select one of the modes: - --only-error-correction — only error correction- --only-assembler — only assembly |
| Error correction | - BayesHammer is used for Illumina reads - IonHammer is used for IonTorrent reads ⚠️ Do not use error correction if input reads have no quality data (e.g., FASTA input files are provided) |
| K-mers | Set one or more k-mer sizes (-k) to be used during assembly. If not specified, SPAdes will choose values automatically based on read length. |
4. Output Files Page
On this page, you can select an output directory:
