QIIME2 IIa: Denoising (sequence quality control) and feature table creation (single-end)
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.
- Author(s):
- Release: 0.2
- License: MIT
- UniqueID: 718df5b9-9cbb-4792-be50-604e18ef0548
QIIME2 workflows
Available workflows
Denoising (using qiime2
's dada2
integration for paired / single end data.
Inputs
- Demultiplexed sequences as a qiime2 aertifact file (
qza
) containing the sequence information. - Metadata table (
tabular
) - Truncation length
- Trimming length (optional)
For the paired end workflow the truncation and trimming length for the reverse reads can / has to be given.
Processing
- Denoising with
qiime2 dada2 denoise-single
/paired
- For each of the three outputs (see below) another tool is started to prepare a corresponding qzv file
- representative sequences
qiime2 feature-table tabulate-seqs
- denoising statistics
qiime2 metadata tabulate
- summary of the feature table
- representative sequences
Outputs
- representative sequences
- denoising statistics
- summary of the feature table (how many sequences are lost in the corresponding steps)