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Download and install the UGENE FULL or NGS package to use this pipeline. |
Use this workflow sample to process raw DNA-seq next-generation sequencing (NGS) data from the Illumina platform. The processing includes:
- Filtration:
- Filtering of the NGS short reads by the CASAVA 1.8 header;
- Trimming of the short reads by quality;
- Mapping:
- Mapping of the short reads to the specified reference sequence (the BWA-MEM tool is used in the sample);
- Post-filtration:
- Filtering of the aligned short reads by SAMtools to remove reads with low mapping quality, unpaired/unaligned reads;
- Removing of duplicated short reads.
The result filtered short reads assembly is provided in the SAM format. Intermediate data files are also available in the output.
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If you haven't used the workflow samples in UGENE before, look at the "How to Use Sample Workflows" section of the documentation. |
Workflow Sample Location
The workflow sample "Raw DNA-Seq processing" can be found in the "NGS" section of the Workflow Designer samples.
Workflow Image
There are two versions of the workflow available. The workflow for single-end reads looks as follows:
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<center> <br> <img src="/wiki/download/attachments/13008929/raw_dnaseq_single-end.png"/> <br> </center> |
The workflow for paired-end short appearance is the following:
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<center> <br> <img src="/wiki/download/attachments/13008929/raw_dnaseq_paired-end.png"/> <br> </center> |