Table 1.

Analytical capability of targeted Next-Generation (DNA) Sequencing (NGS) analysis solutions with respect to clinical and public health microbiology investigative methods.

Solution	Date of Publication/First Release	Upload/Analyse Raw Sequence Data	Reference-Based Mapping	de novo Assembly	Variant Calling	Typing analyses (e.g., MLST)	Comparative Typing Analyses	Multiple Sequence Alignment	Phylogenetic Tree/Network Construction
Generic NGS Analysis Solutions:
BioNumerics a	1992	Yes	Yes	Yes	Yes	No c	Yes	Yes	Yes
CLC Genomics Workbench a	2008	Yes	Yes	Yes	Yes	No	No	Yes	Yes
Galaxy b	2007	Yes	Yes	Yes	Yes	No	No	Yes	Yes
Specific Bacterial NGS Analysis Solutions:
BIGSdb	2010	No	No	No	Yes	Yes	Yes	Yes	Yes
Center for Genomic Epidemiology Web Portal	2011	Yes	No	Yes	Yes	Yes	Yes	No d	Yes
Ridom SeqSphere+ a	2013	Yes	Yes	Yes	Yes	Yes	Yes	Yes	Yes
snp-search	2013	No	No	No	No	No	Yes	No e	Yes

^a Commercial product;

^b Features/analyses described for the default installation and tools available in the Galaxy Tool Shed as of September 2013 only;

^c There is a function to automate typing analyses from first generation but not next-generation sequence data;

^d The Center for Genomic Epidemiology snpTree tool deals only with variant call information and thus multiple sequence alignment sensu stricto is not applicable; however the tool will generate a pseudo-alignment of concatenated single nucleotide polymorphisms;

^e as described for snpTree, snp-search deals only with variant call information but will output a pseudo-alignment of concatenated single nucleotide polymorphisms in FASTA format.