Table 5. The metagenome analysis tools included in this benchmark.

Tool	Version	Taxonomy	Function	Fastq	Zipped	Paired
CLARK	1.1.3	Yes	No	Yes	Yes	Yes
EBI	NA	Yes	Yes	Yes	Yes	Yes
Genometa	0.51	Yes	No	Yes	No	Yes
GOTTCHA	1.0a	Yes (E)	No	Yes	No	Yes
Kraken	0.10.4 beta	Yes	No	Yes	Yes	Yes
LMAT	1.2.4	Yes	Yes	No	No	Yes1
MEGAN2	5.7.0	Yes	Yes	Yes	No	(No)3
MetaPhlAn	2	Yes (E)	No	Yes	Yes	Yes
MetaPhyler	1.25	Yes	No	No	No	Yes4
MG-RAST	3.3.6	Yes (E)	Yes	Yes	Yes	(Yes)5
mOTU	NA	Yes	No	Yes	Yes	Yes
One Codex	NA	Yes (E)	No	Yes	Yes	Yes
QIIME6	1.8.0	Yes	No	Yes	Yes	Yes
Taxator-tk	1.2.1	Yes	No	No	No	Yes7

For each tool, it is shown if it does taxonomic analysis (tools that can also infer Eukaryotic taxa are noted with an “(E)”) and/or functional analysis, and whether it can analyze Fastq files directly, if you can use zipped input files, and if it utilizes paired end information.

¹You need to concatenate the input files with an N between paired reads.

²Input to MEGAN was generated using the aligner Diamond (v0.6.3) from the same group.

³MEGAN supports paired end data. However, Diamond does not explicitly support this.

⁴Each file is treated separately, but the final results can be combined by the tool.

⁵The server recognizes paired end data but seems to treat reads separately.

⁶QIIME is highly flexible and can handle both zipped and unzipped fastq files, and both single- and paired-end reads. However, in this analysis we adapted QIIME to work with fasta output from HMMER and could not use these features.

⁷Although no direct support, the authors provided a way to use the paired information (see Supplementary Material section 2.10 for details).