The workflow sample, described below, takes FASTQ files with metagenomic NGS reads as input and process them as follows:
- Improve reads quality with Trimmomatic
- Provide FastQC reads quality reports
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- Classification:
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- 1. Classify the pre-processed reads with Kraken
2. Classify the assembled contigs with CLARK
3. Classify these reads with DIAMOND (in case of SE reads)
4. Classify these reads with MetaPhlAn2
5. Ensemble the classification output from Kraken, CLARK, and DIAMOND into a CSV file.
6. Improve classification from these tools with WEVOTE.
7. Provide general classification
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- reports
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If you haven't used the workflow samples in UGENEbeforeUGENE before, look at the "How to Use Sample Workflows" section of the documentation. |
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