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QIIME2 Ia: multiplexed data (single-end)

Importing single-end multiplexed data (not demultiplexed yet)

  • Author(s):
  • Debjyoti Ghosh
  • Helmholtz-Zentrum für Umweltforschung - UFZ
  • Release: 0.2
  • License: MIT
  • UniqueID: 951c418e-f57e-491d-af38-f2c44c6089ce

QIIME2 import workflows

Available workflows

Import of fastqsanger.gz data into QIIME artifact files.

Available for:

  • paired / single end data
  • demultiplexed / multiplexed data (the former according to the EMP protocol)

For data that is multiplexed with another protocol the Galaxy cutadapt tool can be use.

Inputs

  • Single end or paired end reads in fastq format.
  • For demultiplexed data all datasets must be in a single (flat) collection (also paired data).

Demultiplexed data

  • Demultiplexed data must follow the naming scheme .+_.+_R[12]_001\.fastq\.gz. Any lane information (in the form of L[0-9][0-9][0-9]_) in the dataset names is automatically removed.

Mulmultiplexed data

  • Multiplexed data in a single or two fastq.gz dataset(s)
  • Barcodes as fastq.gz file
  • Metadata (a table describing the samples) and a metadata parameter (the name of the column that contains the barcode sequences)
  • A boolean determining if there reverse complement of the barcode sequences shoul dbe used

Processing

For demultiplexed data

  1. Lane information is removed from the collection identifiers (using Extract element identifiers, Regex Find And Replace and Relabel identifiers)
  2. Import of sequence data using qiime2 tools import with Casava One Eight Laneless Per Sample Directory Format
  3. Prepare visualisation dataset with qiime2 demux summarize

For multiplexed data

  1. Import sequences and metadata with qiime2 tools import as EMP Paired End Directory Format and Immutable Metadata Format, resp.
  2. Demultiplex the sequences with qiime2 demux emp-paired/paired (using sequences and metadata information)
  3. Prepare visualisation dataset with qiime2 demux summarize

Outputs

  • Sequence data in qza format
  • A corresponding qiime visualization file in qzv format

TODOs

  • The import workflows for multiplexed data currently first convert the metadata into qza and require the user to enter a column as free text. If Galaxy allows for data-column workflow parameters this step can be removed.