Mash: fast genome and metagenome distance estimation using MinHash

Table 3 Sequencing runs and assemblies searched against the Mash RefSeq database

Organism	Tech	Type	NCBI accession	Size (Mbp)	Time (CPU s)	LCA	Best hit
E. coli K12 MG1655	MiSeq	Assembly	(SPAdes)	4.6	2.45	Entero.	E. coli K12 MG1655
E. coli K12 MG1655	PacBio	Assembly	GCA_000801205	4.6	2.66	Entero.	E. coli K12 MG1655
E. coli DH1	ABI 3730	Reads	(Trace Archive)	60	17.08	Entero.	E. coli DH1
E. coli K12 MG1655	454	Reads	SRR797242	233	57.12	Entero.	E. coli K12 MG1655
E. coli K12 MG1655	Ion PGM	Reads	SRR515925	407	72.01	E. coli	E. coli K12 1655
E. coli K12 MG1655	MiSeq	Reads	SRR1770413	387	72.01	Entero.	E. coli KLY
E. coli K12 MT203	HiSeq	Reads	SRR490124	2155	369.86	E. coli	E. coli GCF_000833635
E. coli K12 MG1655	PacBio	Reads	SRR1284073	397	77.96	E. coli	E. coli XH140A GCF_000226585
E. coli K12 MG1655	MinION	1D	ERR764952..55	248	55.52	Entero.	E. coli O113 H21
E. coli K12 MG1655	MinION	2D	ERR764952..55	134	27.82	E. coli	E. coli GCF_000953515
B. anthracis Ames	MinION	1D + 2D	SRR2671867	210	44.66	B. anthracis	B. anthracis str. Carbosap
B. cereus ATCC 10987	MinION	1D + 2D	SRR2671868	266	76.85	B. cereus ATCC 10987	B. cereus ATCC 10987
Zaire ebolavirus	MinION	1D + 2D	ERR1050070	8.7	2.06	Zaire ebolavirus	Zaire ebolavirus Mayinga

In all cases, Mash search required 21 MB of RAM for genome assemblies and 209 MB of RAM for sequencing runs (due to the additional Bloom filter overhead). Organism: source strain. Tech: Sequencing technology ABI 3730, 454 GS FLX, Illumina MiSeq, Illumina HiSeq, Ion PGM, PacBio RSII, Oxford Nanopore MinION. Type: Assembly, reads, 1D and 2D nanopore reads. NCBI accession: NCBI accession of the dataset or reads. The SPAdes [63] assembly was derived from the MiSeq reads. Size: total dataset size in Mbp. LCA: lowest common ancestor classification based on the NCBI taxonomy and the resulting hits within a significance tolerance of the best. In several cases, the LCA is at the family level (Enterobacteriaceae) due to significant Mash hits to both E. coli and S. sonnei species. This is a known species naming conflict within the NCBI taxonomy, with some genomes sharing ANI >98 % between these species. Best hit: reports the smallest significant distance reported

ISSN: 1474-760X