Genomics of Corynebacterium striatum, an emerging multidrug-resistant pathogen of immunocompromised patients
January 2018
Authors:
K. Nudel, X. Zhao, S. Basu, X. Dong, et al.
Info:
Scientists from Harvard Medical School and other institutions used whole genome sequencing and MALDI/TOF to analyze seven C. striatum infections, all resistant to multiple drugs. They found that three of the pathogens were related, and that complex resistance profiles could be spread by a single recombination event. BluePippin was used for size-selecting libraries prior to PacBio sequencing.
Citation:
Clinical Microbiology and Infection
Isoform Sequencing and State-of-Art Applications for Unravelling Complexity of Plant Transcriptomes
January 2018
Authors:
Dong An, Hieu X. Cao, Changsheng Li, Klaus Humbeck and Wenqin Wang
Info:
In this paper, researchers offer best practices for using the Iso-Seq method with PacBio sequencing to analyze plant transcriptomes. They recommend BluePippin for size partitioning, noting that it allows for more even representation of cDNAs even when their lengths vary.
Citation:
Genes 2018, 9(1), 43
doi:10.3390/genes9010043
Finding Nemo: Hybrid assembly with Oxford Nanopore and Illumina reads greatly improves the Clownfish (Amphiprion ocellaris) genome assembly
January 2018
Authors:
Mun Hua Tan, Christopher Austin, Michael Hammer, Yin Peng Lee, Laurence Croft, Han Ming Gan
Info:
This paper presents the first hybrid genome assembly of Amphiprion ocellaris, the clown anemonefish. The team combined data from Illumina and Oxford Nanopore sequencing, reducing the number of scaffolds compared to a short-read-only assembly by 94%. BluePippin was used to select large DNA fragments for nanopore sequencing.
Citation:
GigaScience
doi: 10.1093/gigascience/gix137
Characterization of plasmids harboring blaCTX-M and blaCMY genes in E. coli from French broilers
January 2018
Authors:
Fabrice Touzain, Laetitia Le Devendec, Claire de Boisséson, Sandrine Baron, et al.
Info:
In this study of avian E. coli collected from slaughterhouses or diseased broilers, scientists analyzed resistance to extended-spectrum cephalosporins. Sequencing was performed with Illumina and PacBio platforms, and the team used BluePippin for size selection in the PacBio pipeline.
Citation:
PLoS One
doi: 10.1371/journal.pone.0188768
Nemertean and phoronid genomes reveal lophotrochozoan evolution and the origin of bilaterian heads
December 2017
Authors:
Yi-Jyun Luo, Miyuki Kanda, Ryo Koyanagi, Kanako Hisata, et al.
Info:
Scientists from the Okinawa Institute of Science and Technology Graduate University and Okayama University in Japan generated draft genomes and transcriptomes of ribbon worms and horseshoe worms, with major implications for understanding the evolution of these species. For this work, the team used SageELF and BluePippin to perform automated size selection for mate-pair libraries in an Illumina workflow.
Citation:
Nature Ecology & Evolution volume 2, pages141–151 (2018)
doi:10.1038/s41559-017-0389-y