Table 1:

Available tools in ASaiM

Section	Subsection	Tools
File and meta tools	Data retrieval	EBISearch [20], ENASearch [21], SRA Tools
	Text manipulation	Tools from Galaxy ToolShed
	Sequence file manipulation	Tools from Galaxy ToolShed
	BAM/SAM file manipulation	SAM tools [22-24]
	BIOM file manipulation	BIOM-Format tools [25]
Genomics tools	Quality control	FastQC [26], PRINSEQ [27], Trim Galore! [28, Trimmomatic [29], MultiQC [30]
	Clustering	CD-Hit [31], Format CD-HIT outputs
	Sorting and prediction	SortMeRNA [32], FragGeneScan [33]
	Mapping	BWA [34], Bowtie [35]
	Similarity search	NCBI Blast+ [36, 37], Diamond [38]
	Alignment	HMMER3 [39]
Microbiota dedicated tools	Metagenomics data manipulation	VSEARCH [11], Nonpareil [40]
	Assembly	MEGAHIT [41], metaSPAdes [42], metaQUAST [43], VALET [44]
	Metataxonomic sequence analysis	Mothur [3], QIIME [2]
	Taxonomy assignation on WGS sequences	MetaPhlAn2 [45], Format MetaPhlan2, Kraken [10]
	Metabolism assignation	HUMAnN2 [46], Group HUMAnN2 to GO slim terms [47], Compare HUMAnN2 outputs, PICRUST [48], InterProScan
	Combination of functional and taxonomic results	Combine MetaPhlAn2 and HUMAnN2 outputs
	Visualization	Export2graphlan [49], GraPhlAn [50], KRONA [51]

This table presents the tools, organized in sections and subsections to help users. A more detailed table of the available tools and some documentation can be found in the online documentation (http://asaim.readthedocs.io/en/latest/tools/).