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Seqsphere v 6

Manufactured by Ridom
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Sourced in Germany

Ridom SeqSphere+ v. 6.0.2 is a software application designed for molecular typing and analysis of bacterial isolates. It provides tools for sequence-based characterization, comparison, and interpretation of genomic data.

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SeqSphere+

2 protocols using seqsphere v 6

1

Comparative Genomic Analysis of Serovars

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To provide gene-by-gene comparison, we aligned all of our closed genomes based on serovar using MAUVE aligner version 20150226 using the progressive algorithm with default settings, and phages were identified using PHASTER (32) . Any unique genomic regions, phages, and plasmids identified were imported into Ridom SeqSphere + v. 6.0.2 (Ridom GmbH, Munster, Germany) (33) and used as a reference to interrogate the 201 short read isolate assemblies used in this study for presence or absence.
Haendiges J., Davidson G.R., Pettengill J.B., Reed E., Blessington T., Miller J.E., Anderson N., Myoda S., Brown E.W., Zheng J., Tikekar R.V., & Hoffmann M. (2021). Genomic Evidence of Environmental and ResidentSalmonellaSenftenberg and Montevideo Contamination in the Pistachio Supply-chain.
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2

Comparative Genomic Analysis Protocol

Check if the same lab product or an alternative is used in the 5 most similar protocols
To provide gene-by-gene comparison, we aligned all of our closed genomes based on serovar using MAUVE aligner version 20150226 using the progressive algorithm with default settings, and phages were identified using PHASTER [32 ]. Any unique genomic regions, phages, and plasmids identified were imported into Ridom SeqSphere+ v. 6.0.2 (Ridom GmbH, Munster, Germany) [33 (link)] and used as a reference to interrogate the 201 short read isolate assemblies used in this study for presence or absence.
Haendiges J., Davidson G.R., Pettengill J.B., Reed E., Ramachandran P., Blessington T., Miller J.D., Anderson N., Myoda S., Brown E.W., Zheng J., Tikekar R, & Hoffmann M. (2021). Genomic evidence of environmental and resident Salmonella Senftenberg and Montevideo contamination in the pistachio supply-chain. PLoS ONE, 16(11), e0259471.
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