Large-scale sequence comparisons with <i>sourmash</i>

Pierce, Nicholas; Irber, Luiz; Reiter, Taylor; Brooks, Phillip T.; Brown, C. Titus

doi:10.1101/687285

Cited by 29 publications

(48 citation statements)

References 19 publications

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“…Genomes corresponding to novel species were identified as those with identity <95% or coverage <80% when compared with known genomes (BLAST with nt) and three recent catalogs that include environmental and human microbiome assembled genomes [31][32][33] (with Mash 68 ). The genomes were hierarchically clustered (single linkage with Mash distance 68 ) to identify species-level clusters at 95% identity, and genus-level taxonomic classification was obtained using sourmash 69 . Similarly, novel circular plasmids were identified by comparing to the PLSDB 36 database with Mash distance and identifying clusters at 99% identity (single linkage) with no known sequence.…”

Section: © the Author(s) 2020mentioning

confidence: 99%

Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment

Li¹,

Bertrand²,

Kwah³

et al. 2020

Nat Med

168

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Although disinfection is key to infection control, the colonization patterns and resistomes of hospital-environment microbes remain underexplored. We report the first extensive genomic characterization of microbiomes, pathogens and antibiotic resistance cassettes in a tertiary-care hospital, from repeated sampling (up to 1.5 years apart) of 179 sites associated with 45 beds. Deep shotgun metagenomics unveiled distinct ecological niches of microbes and antibiotic resistance genes characterized by biofilm-forming and human-microbiome-influenced environments with corresponding patterns of spatiotemporal divergence. Quasi-metagenomics with nanopore sequencing provided thousands of high-contiguity genomes, phage and plasmid sequences (>60% novel), enabling characterization of resistome and mobilome diversity and dynamic architectures in hospital environments. Phylogenetics identified multidrug-resistant strains as being widely distributed and stably colonizing across sites. Comparisons with clinical isolates indicated that such microbes can persist in hospitals for extended periods (>8 years), to opportunistically infect patients. These findings highlight the importance of characterizing antibiotic resistance reservoirs in hospitals and establish the feasibility of systematic surveys to target resources for preventing infections.

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Section: © the Author(s) 2020mentioning

confidence: 99%

Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment

Li¹,

Bertrand²,

Kwah³

et al. 2020

Nat Med

168

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“…Detection and classification of 16S rRNA gene fragments were performed with SortMeRNA (50) and the RDP classifier (51). K-mer profiling was performed with sourmash (52,53). All statistical analyses were done in R using the vegan To profile the viral communities in these 16 samples and to compare two common techniques for viral community analyses, paired total metagenomes and viral size-fraction metagenomes (viromes) were generated from each sample (with the exception of one April sample, PN-L, that did not yield enough DNA to perform virome sequencing).…”

Section: Read Processing and Data Analysismentioning

confidence: 99%

Viromes outperform total metagenomes in revealing the spatiotemporal patterns of agricultural soil viral communities

Santos‐Medellín

Zinke

Horst

et al. 2020

Preprint

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Viruses are abundant yet understudied members of soil environments that influence terrestrial biogeochemical cycles. Here, we characterized the dsDNA viral diversity in biochar-amended agricultural soils at the pre-planting and harvesting stages of a tomato growing season via paired total metagenomes and viromes. Size fractionation prior to DNA extraction reduced sources of non-viral DNA in viromes, enabling the recovery of a vaster richness of viral populations (vOTUs), greater viral taxonomic diversity, broader range of predicted hosts, and better access to the rare virosphere, relative to total metagenomes, which tended to recover only the most persistent and abundant vOTUs. Of 2,961 detected vOTUs, 2,684 were recovered exclusively from viromes, while only three were recovered from total metagenomes alone. Both viral and microbial communities differed significantly over time, suggesting a coupled response to rhizosphere recruitment processes and nitrogen amendments. Viral communities alone were also structured along a spatial gradient. Overall, our results highlight the utility of soil viromics and reveal similarities between viral and microbial community dynamics throughout the tomato growing season yet suggest a partial decoupling of the processes driving their spatial distributions, potentially due to differences in dispersal, decay rates, and/or sensitivities to soil heterogeneity.

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“…Kmer-db reports even faster compute times than Mash, largely through an improved k-mer hash and parallel implementation (Deorowicz et al 2019). sourmash adds some functionality to Mash and implements scaled, rather than thresholded, numbers of retained kmer hashes (Pierce et al 2019). This method can enable comparisons of datasets that differ greatly in size, but slows down analysis (Pierce et al 2019).…”

Section: Comparison With Other Alignment-free Methodsmentioning

confidence: 99%

“…sourmash adds some functionality to Mash and implements scaled, rather than thresholded, numbers of retained kmer hashes (Pierce et al 2019). This method can enable comparisons of datasets that differ greatly in size, but slows down analysis (Pierce et al 2019). We checked the performance of these other tools against Mash for the simulated data in this study, but neither sourmash nor kmer-db showed advantage over Mash.…”

Section: Comparison With Other Alignment-free Methodsmentioning

confidence: 99%

Alignment-free methods for polyploid genomes: quick and reliable genetic distance estimation

VanWallendael

Álvarez

2020

Preprint

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Polyploid genomes pose several inherent challenges to population genetic analyses. While alignment-based methods are fundamentally limited in their applicability to polyploids, alignment-free methods bypass most of these limits. We investigated the use of Mash, a k-mer analysis tool that uses the MinHash method to reduce complexity in large genomic datasets, for basic population genetic analyses of polyploid sequences. We measured the degree to which Mash correctly estimated pairwise genetic distance in simulated diploid and polyploid short-read sequences with various levels of missing data. Mash-based estimates of genetic distance were comparable to alignment-based estimates, and were less impacted by missing data. We also used Mash to analyze publicly available short-read data for three polyploid and one diploid species, then compared Mash results to published results. For both simulated and real data, Mash accurately estimated pairwise genetic differences for polyploids as well as diploids as much as 476 times faster than alignment-based methods, though we found that Mash genetic distance estimates could be biased by per-sample read depth. Mash may be a particularly useful addition to the toolkit of polyploid geneticists for rapid confirmation of alignment-based results and for basic population genetics in reference-free systems with poor quality DNA.

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Large-scale sequence comparisons with sourmash

Cited by 29 publications

References 19 publications

Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment

Cartography of opportunistic pathogens and antibiotic resistance genes in a tertiary hospital environment

Viromes outperform total metagenomes in revealing the spatiotemporal patterns of agricultural soil viral communities

Alignment-free methods for polyploid genomes: quick and reliable genetic distance estimation

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