Installing a local copy of NextStrain for nCov19 with Conda
Alberta Children's Hospital Research Institute - Bioinformatics
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4y ago
p.p1 {margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Menlo; color: #000000} span.s1 {font-variant-ligatures: no-common-ligatures} 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
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Nanopore bacterial genome assemblies
Alberta Children's Hospital Research Institute - Bioinformatics
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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
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Hybrid PacBio + Illumina assembly: turning Unicycler on its head
Alberta Children's Hospital Research Institute - Bioinformatics
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5y ago
p.p1 {margin: 0.0px 0.0px 0.0px 0.0px; font: 11.0px Menlo; color: #FFFFFF} span.s1 {font-variant-ligatures: no-common-ligatures; color: #FFFFFF} 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
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