Sequencing and Assembly of Mucispirillum schaedleri Genome

Mucispirillum schaedleri ASF 457 variant MCS was provided to Bärbel Stecher by Charles River Laboratories, Inc. (Wilmington, MA, USA). Nucleic acids were extracted using a phenol-chloroform-based extraction method (80 (link)). DNAs were sequenced using the Illumina HiSeq2000 with 3-kb mate pair libraries and MinION technology (Oxford Nanopore Technologies, Oxford, United Kingdom). Illumina data were quality filtered with prinseq-lite (81 (link)), and MinION data were filtered with poretools (82 (link)) and prinseq-lite. De novo genome assembly was performed using SPAdes (83 (link)).

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Loy A., Pfann C., Steinberger M., Hanson B., Herp S., Brugiroux S., Gomes Neto J.C., Boekschoten M.V., Schwab C., Urich T., Ramer-Tait A.E., Rattei T., Stecher B, & Berry D. (2017). Lifestyle and Horizontal Gene Transfer-Mediated Evolution of Mucispirillum schaedleri, a Core Member of the Murine Gut Microbiota. mSystems, 2(1), e00171-16.

Publication 2017

HiSeq2000 MinION technology prinseq-lite MinION

Chloroform Dnas Genome Mucispirillum schaedleri Nucleic acids Phenol River

Corresponding Organization :

Other organizations : University of Vienna, Ludwig-Maximilians-Universität München, German Center for Infection Research, University of Nebraska–Lincoln, Wageningen University & Research

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Variable analysis

independent variables

Nucleic acids extraction method (phenol-chloroform-based extraction)
Sequencing technologies (Illumina HiSeq2000 with 3-kb mate pair libraries and MinION)
Data filtering methods (prinseq-lite for Illumina data, poretools and prinseq-lite for MinION data)
Genome assembly method (SPAdes)

dependent variables

Sequencing data quality
Genome assembly quality

control variables

Not explicitly mentioned

controls

No positive or negative controls were explicitly mentioned in the provided information.

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