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Monthly Archives: February 2018
Podcast: Blogger Keith Robison on the State of Sequencing
A new podcast from Mendelspod takes a look at the state of sequencing in 2018. It’s a lively and interesting discussion about the current and future landscape of genomics between host Theral Timpson and Keith Robison, founder of the Omics! … more »
Assembly and RNA‐free annotation of highly heterozygous genomes: The case of the thick‐billed murre (Uria lomvia)
January 2018 Authors: Anna Tigano, Timothy Sackton, and Vicki Friesen Info: Researchers at Queen’s University and Harvard teamed up for an effort to assemble the highly heterozygous genome of an arctic colonial seabird. The found that the platanus assembler outperformed … more »
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At AGBT, Scientists Offer Data on Size Selection for HMW DNA
Even Orlando’s sky-high humidity can’t get us down during a fast-paced AGBT meeting where size selection and HMW DNA have been front and center since the opening session. Last night we enjoyed a plenary talk from Ami Bhatt, a scientist … more »
SageELF Enables Targeted RenSeq Capture for PacBio Sequencing
We’ve had targeted capture on the brain lately as we work with collaborators to put the finishing touches on our HLS-CATCH method for selecting large genomic elements using Cas9 guides and the SageHLS system. So today, we wanted to revisit … more »
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 … more »
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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 … more »
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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 … more »
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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 … more »
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Fireworks, Genomics, and HLS-CATCH at AGBT in Orlando
The regular Super Bowl may have gone down last weekend, but the genomics Super Bowl is still to come with next week’s Advances in Genome Biology & Technology meeting in Orlando. The Sage Science team can’t wait. AGBT is our … more »