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dada2 amplicon analysis pipeline - for paired end data

dada2 amplicon analysis for paired end data The workflow has three main outputs: - the sequence table (output of makeSequenceTable) - the taxonomy (output of assignTaxonomy) - the counts which allow to track the number of sequences in the samples through the steps (output of sequence counts)

  • Author(s):
  • Matthias Bernt
  • UFZ Leipzig
  • Release: 0.2
  • License: MIT
  • UniqueID: 11d717f8-92ef-4dd7-bda7-c193175fece2

Dada2: amplicon analysis for paired end data

Inputs dataset

  • Paired input data paired input collection in FASTQ format

Inputs values

  • Read length forward/reverse reads length of the forward/reverse reads to which they should be truncated in the filter and trim step
  • Pool samples pooling may increase sensitivity
  • Reference database that should be used for taxonomic assignment

Processing

The workflow follows the steps described in the dada2 tutorial.

As a first step the input collection is sorted. This is important because the dada2 step outputs a collection in sorted order. If the input collection would not be sorted then the mergePairs step samples would be mixed up.

  • FilterAndTrim Quality control by filtering and trimming reads
  • QualityProfile is called before and after the FilterAndTrim step
  • Unzip Collection separates forward and reverse reads (the next steps are evaluated separately on forward and reverse reads)
  • learnErrors learn error rates
  • dada filter noisy reads
  • mergePairs merge forward and reverse reads
  • makeSequenceTable create the sequence table
  • removeBimeraDenovo remove chimeric sequencs
  • assignTaxonomy assign taxonomic information from a reference data base

TODO

Some possibilities to extend/improve the workflow

  • output BIOM
  • use ASV1, ... in sequence table and taxonomy output, and output additional fasta
  • allow to use custom taxonomy / make it optional