qiime2-II-denoising/IIa-denoising-se
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Tests Use DADA2 for sequence quality control. DADA2 is a pipeline for detecting and correcting (where possible) Illumina amplicon sequence data. As implemented in the q2-dada2 plugin, this quality control process will additionally filter any phiX reads (commonly present in marker gene Illumina sequence data) that are identified in the sequencing data, and will filter chimeric sequences.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| Demultiplexed sequences | #main/Demultiplexed sequences | Demultiplexed sequences in qza format |
|
| Metadata | #main/Metadata | Tab separated metadata file |
|
| Trimming length | #main/Trimming length | Number of bases at the 5' end that should be removed. Default: 0. |
|
| Truncation length | #main/Truncation length | Length to which the sequence sould be truncated. Will remove bases from the 3' end. |
|
Steps
| ID | Name | Description |
|---|---|---|
| 4 | Denoising the datasets | qiime2 dada2 denoise-paired Denoise and dereplicate paired-end sequences Small insight: if the denoising percentage is lower or poorer, reduce 'trunc_q: Int' from 2 to 1. toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__dada2__denoise_single/qiime2__dada2__denoise_single/2024.10.0+q2galaxy.2024.10.0 |
| 5 | Tabulate DADA2 denoised representative sequences | qiime2 feature-table tabulate-seqs View sequence associated with each feature toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_table__tabulate_seqs/qiime2__feature_table__tabulate_seqs/2024.10.0+q2galaxy.2024.10.0 |
| 6 | Tabulate DADA2 statistical metadata | qiime2 metadata tabulate Interactively explore Metadata in a table toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__metadata__tabulate/qiime2__metadata__tabulate/2024.10.0+q2galaxy.2024.10.0 |
| 7 | Summing up the dada2 output table | qiime2 feature-table summarize Summarize table toolshed.g2.bx.psu.edu/repos/q2d2/qiime2__feature_table__summarize/qiime2__feature_table__summarize/2024.10.0+q2galaxy.2024.10.0 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| DADA2 output table | #main/DADA2 output table | n/a |
|
| DADA2 representative sequences list visualisation | #main/DADA2 representative sequences list visualisation | n/a |
|
| DADA2 statistics visualisation | #main/DADA2 statistics visualisation | n/a |
|
| Denoising output table | #main/Denoising output table | n/a |
|
| Denoising statistics | #main/Denoising statistics | n/a |
|
| Representative denoised sequences | #main/Representative denoised sequences | n/a |
|
Version History
v0.2 (earliest) Created 30th May 2024 at 11:35 by WorkflowHub Bot
Updated to v0.2
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v0.2b2a2493
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Views: 1501 Downloads: 212 Runs: 0
Created: 30th May 2024 at 11:35
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