SLIM: a flexible web application for the reproducible processing of environmental DNA metabarcoding data

BMC Bioinformatics

Table 1 List of available modules in SLIM and planned integration

Processing step	Module	Availability	References
SRA downloader	SRA	planned	Short Read Archive tools (https://github.com/ncbi/sra-tools)
Demultiplexing	DTD	yes	https://github.com/yoann-dufresne/DoubleTagDemultiplexer
Mistag-filtering	mistag	planned	[33]
Denoising / ASV inference	DADA2	planned	[15]
Reads joining	PANDAseq	yes	[37]
	CASPER	yes	[38]
	VSEARCH	yes	[31]
Chimera-removal	VSEARCH	yes	[31]
OTU clustering	VSEARCH	yes	[31]
OTU clustering	SWARM	yes	[39]
Taxonomic assignement	VSEARCH	yes	[31]
	CREST	planned	[24]
	IDTAXA	planned	[34]
Post-processing	LULU	yes	[35]
Post-processing	Biotic Indices	planned	[36]

ISSN: 1471-2105