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Table 1 Comparison of the pipeline ASAP 2 with other tools in terms of processes that involve manual interference

From: ASAP 2: a pipeline and web server to analyze marker gene amplicon sequencing data automatically and consistently

  QIIME 2 DADA 2 MetaAmp (OTU-based) MetaAmp ASV-based) ASAP 2
Feature ASV ASV OTU ASV ASV
Supported formats All * Only demultiplexed sequences Only demultiplexed sequences Only demultiplexed sequences All*
Barcode orientation identification Manual Manual NA** NA** Auto
Combination of multiple projects Manually merge feature tables Manually merge feature tables OTUs cannot be combined Demultiplexed data as input Auto merge feature tables
High-quality region identification Manual Manual NA*** Manual Auto
Resampling depth Manual Manual Manual Manual Auto
  1. *Multiplexed/demultiplexed, barcode-inside/barcode-outside, sequence/feature table
  2. **It requires demultiplexed data, so barcode orientation identification is not required
  3. ***It does not apply error correction for ASV, so region selection is not required