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

BMC Bioinformatics

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

	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

*Multiplexed/demultiplexed, barcode-inside/barcode-outside, sequence/feature table
**It requires demultiplexed data, so barcode orientation identification is not required
***It does not apply error correction for ASV, so region selection is not required

ISSN: 1471-2105