Alberta Children's Hospital Research Institute - Bioinformatics
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This blog provides updates on the happenings at the Bioinformatics Support Services of the Alberta Children's Hospital Research Institute. This includes a mix of technical information of use to other bioinformaticians, and practical information about services for both bench researchers and clinicians. Opinions expressed here are solely my (Paul Gordon) own, and should not be construed as..
Alberta Children's Hospital Research Institute - Bioinformatics
4y ago
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NextStrain is great software for visualizing the relationships between isolates of a virus. It is used for influenza, but also for other viruses and they have made a system configured for the novel coronavirus that has emerged out of Wuhan, China. For most people ..read more
Alberta Children's Hospital Research Institute - Bioinformatics
4y ago
tl;dr You should be able to get 99.95%+ DNA genome assembly accuracy from an Oxford Nanopore Technologies MinION device using the combination of Guppy modified base high accuracy base calling + Flye genome assembly w/ 2 rounds of polishing + 4 rounds of racon polishing + one round of medaka polishing. Steps to make a hybrid assembly with Illumina (SPAdes + pilon) are also included.
On a properly ..read more
Alberta Children's Hospital Research Institute - Bioinformatics
5y ago
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tl;dr Unicycler is an amazing program that does a great job of assembling microbial genomes from short and long reads. In hybrid assembly mode, short reads are assembled into contigs, then these are spanned using long reads such as those from ..read more