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
Genome-wide DNA methylation profiling using the methylation-dependent restriction enzyme LpnPI
December 2017
Authors:
Ruben Boers, Joachim Boers, Bas de Hoon, Christel Kockx, et al.
Info:
Scientists at Erasmus Medical Center determined that analysis of genome-wide methylation is challenging when fragment sizes are too small and that better epigenetic results are possible with MeD-seq. The enzyme LpnPI, they found, “is blocked by a fragment size smaller than 32 bp.” The team used PippinHT to purify PCR products prior to sequencing on the Illumina HiSeq 2500.
Citation:
Genome Research
https://genome.cshlp.org/content/28/1/88
Mapping and phasing of structural variation in patient genomes using nanopore sequencing
November 2017
Authors:
Mircea Cretu Stancu, Markus van Roosmalen, Ivo Renkens, Marleen Nieboer, et al.
Info:
Scientists used the Oxford MinION nanopore sequencer with a novel pipeline, NanoSV, to detect structural variants from the genomes of two patients. They found that long reads are better than short reads at detecting events such as de novo chromothripsis rearrangements. The team used PippinHT for size-selecting libraries prior to sequencing.
Citation:
Nature Communications 8: 1326 (2017)
doi: 10.1038/s41467-017-01343-4