qiime2-II-denoising/IIa-denoising-se
v0.2

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Workflow Type: Galaxy

Tests Passing

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.

SEEK ID: https://workflowhub.eu/workflows/892?version=1

Inputs

ID	Name	Description	Type
Demultiplexed sequences	#main/Demultiplexed sequences	Demultiplexed sequences in qza format	File
Metadata	#main/Metadata	Tab separated metadata file	File
Trimming length	#main/Trimming length	Number of bases at the 5' end that should be removed. Default: 0.	int
Truncation length	#main/Truncation length	Length to which the sequence sould be truncated. Will remove bases from the 3' end.	int

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/2023.5.0+q2galaxy.2023.5.0.2
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/2023.5.0+q2galaxy.2023.5.0.2
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/2023.5.0+q2galaxy.2023.5.0.2
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/2023.5.0+q2galaxy.2023.5.0.2

Outputs

ID	Name	Description	Type
DADA2 output table	#main/DADA2 output table	n/a	File
DADA2 representative sequences list visualisation	#main/DADA2 representative sequences list visualisation	n/a	File
DADA2 statistics visualisation	#main/DADA2 statistics visualisation	n/a	File
Denoising output table	#main/Denoising output table	n/a	File
Denoising statistics	#main/Denoising statistics	n/a	File
Representative denoised sequences	#main/Representative denoised sequences	n/a	File