MetaComp: comprehensive analysis software for comparative meta-omics including comparative metagenomics

BMC Bioinformatics

Table 1 Input data for available comparative meta-omic tools

Tool	Meta-omics	Input Format	Hypothesis	Multiple Testing	Reference
	Data^a		Testing Modes^b	Correction^c
XIPE-TOTEC	GS	SEED output, APM format.	TST	Bonferroni and FDR	[13]
MEGAN6	GM, GR, GS,	BLAST, RDP classifier, SIN	NA	NA	[14]
	TM, TS	-A and STAMP outputs; AP
	and P	-M in CSV format, BIOM,
		DAA and SAM files.
IMG/M4	GR, and GS	MG-RAST and BLAST out	MST and TST	NA	[15]
		-puts; APM, BIOM, fasta
		and fastq files.
STAMP	GM, GR, GS,	MG-RAST, IMG/M, CoMet	MST, TGST and	Bonferroni, FDR and	[16]
	TM, TS	and RITA outputs; APM a	TST	Šidák
	and P*	-nd BIOM files.
Metastats and	GM, GR, GS,	APM and BIOM files.	MST and TST	Bonferroni and FDR	[17, 19]
metagenomeSeq	TM and TS
Fantom	GR, GS	CAMERA, MG-RAST and	TGST and TST	Bonferroni and FDR	[18]
		IMG/M outputs.
XCMS	B	cdf, mzData, mzData.XML,	MST and TGST	FDR	[20]
		mzXML, netCDF, wiff
		and wiff.scan
MetaComp	GM, GR, GS,	BLAST, HMMscan, IMG/M,	MST, TGST and	Bonferroni and FDR	This work
	TM, TS, P	MG-RAST, MZmine, Kraken	TST
	and B	and PhymmBL outputs; APM
		and BIOM files.

^aAsterisk (*) denotes that the data types are not designed to be processed but compatible with this tool as an input. Abbreviation of meta-omics data types: GM: amplicon sequenced metagenomic marker gene sequeneces; GR: amplicon sequenced 16S rRNA sequences; GS: shotgun sequenced metagenomic sequences; TM: amplicon sequenced metatranscriptomic marker gene sequences; TS: shotgun sequenced metatranscriptomic sequences; P: metaproteomic sequences. B: metabolomic data
^bAbbreviation of hypothesis testing modes. MST: multi-sample test; TGST: two-group sample test; TST: two-sample test
^cFDR denotes for false discovery rate correction

ISSN: 1471-2105