Warning |
---|
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.
Tip | ||
---|---|---|
| ||
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:
HTML |
---|
<center> <br> <img src="/wiki/download/attachments/14058845/Raw DNA-Seq Processing.png"/> <br> </center> |
The workflow for paired-end short appearance is the following:
HTML |
---|
<center> <br> <img src="/wiki/download/attachments/14058845/Raw DNA-Seq Processing_1.png"/> <br> </center> |
Workflow Wizard
The wizard for single-end reads has 5 page.
Input data: On this page you must input FASTQ file(s).
HTML <center> <br> <img src="/wiki/download/attachments/14058845/Raw DNA-Seq Processing_2.png"/> <br> </center>
Pre-processing: On this page you can modify filtration parameters.
HTML <center> <br> <img src="/wiki/download/attachments/14058845/Raw DNA-Seq Processing_3.png"/> <br> </center>
Mapping: On this page you must input reference and optionally modify advanced parameters.
HTML <center> <br> <img src="/wiki/download/attachments/14058845/Raw DNA-Seq Processing_4.png"/> <br> </center>
Post-processing: On this page you can modify post-processing parameters.
HTML <center> <br> <img src="/wiki/download/attachments/14058845/Raw DNA-Seq Processing_5.png"/> <br> </center>
Output data: On this page you must input output parameters.
HTML <center> <br> <img src="/wiki/download/attachments/14058845/Raw DNA-Seq Processing_6.png"/> <br> </center>
The wizard for paired-end reads has 5 page.
Input data: On this page you must input FASTQ file(s).
HTML <center> <br> <img src="/wiki/download/attachments/14058845/Raw DNA-Seq Processing_7.png"/> <br> </center>
Pre-processing: On this page you can modify filtration parameters.
HTML <center> <br> <img src="/wiki/download/attachments/14058845/Raw DNA-Seq Processing_8.png"/> <br> </center>
Mapping: On this page you must input reference and optionally modify advanced parameters.
HTML <center> <br> <img src="/wiki/download/attachments/14058845/Raw DNA-Seq Processing_9.png"/> <br> </center>
Post-processing: On this page you can modify post-processing parameters.
HTML <center> <br> <img src="/wiki/download/attachments/14058845/Raw DNA-Seq Processing_10.png"/> <br> </center>
Output data: On this page you must input output parameters.
HTML <center> <br> <img src="/wiki/download/attachments/14058845/Raw DNA-Seq Processing_11.png"/> <br> </center>