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Month: January 2020

Genome annotation with prokka

Genome annotation with prokka

Why use Prokka? First, because in a benchmark test it has been shown to be as or more accurate at reproducing known annotation than RAST or xBASE2 in most annotation categories. Second, because it’s fast and you can run it on a standard laptop within a short time, while sending your genome out for annotation to the RAST server can take a day or so to return. If you’re interested in learning to use the RAST server, search the site…

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Sequence Assembly

Sequence Assembly

For today’s class, I have prepared a shared dropbox folder that contains the following items: sequence reads from one of the better chloroplast genome samples generated with our Ion Torrent instrument ERR008613 (a set of paired end Illumina sequence reads from ends of 200bp E. coli fragments) ERR022075 (a set of paired end Illumina sequence reads from ends of 600bp E. coli fragments) sets of PacBio CCS and CLR reads for E. coli In the first part of the exercise,…

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NGS QC

NGS QC

In this exercise we will focus primarily on quality analysis and quality control of Illumina sequencing data, since that is the type of NGS data you are currently most likely to encounter in new datasets. You can view older versions of this exercise for tips on how to handle Ion Torrent or 454 data if you encounter that in your work. What sequence data looks like — the FASTQ file NGS read files tend to be distributed in *.fastq format. To…

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