<![CDATA[BOL: poRe: an R package for the visualization and analysis of nanopore sequencing data]]> https://bioinformaticsonline.com/bookmarks/view/34396/pore-an-r-package-for-the-visualization-and-analysis-of-nanopore-sequencing-data? https://bioinformaticsonline.com/bookmarks/view/34396/pore-an-r-package-for-the-visualization-and-analysis-of-nanopore-sequencing-data Thu, 23 Nov 2017 09:55:57 -0600 https://bioinformaticsonline.com/bookmarks/view/34396/pore-an-r-package-for-the-visualization-and-analysis-of-nanopore-sequencing-data <![CDATA[poRe: an R package for the visualization and analysis of nanopore sequencing data]]> Motivation: The Oxford Nanopore MinION device represents a unique sequencing technology. As a mobile sequencing device powered by the USB port of a laptop, the MinION has huge potential applications. To enable these applications, the bioinformatics community will need to design and build a suite of tools specifically for MinION data.

Results: Here we present poRe, a package for R that enables users to manipulate, organize, summarize and visualize MinION nanopore sequencing data. As a package for R, poRe has been tested on Windows, Linux and MacOSX. Crucially, the Windows version allows users to analyse MinION data on the Windows laptop attached to the device.

Availability and implementation: poRe is released as a package for R at http://sourceforge.net/projects/rpore/ . A tutorial and further information are available at https://sourceforge.net/p/rpore/wiki/Home/

Contact:mick.watson@roslin.ed.ac.uk

Address of the bookmark: https://academic.oup.com/bioinformatics/article/31/1/114/2365693

]]> Jit https://bioinformaticsonline.com/bookmarks/view/34396/pore-an-r-package-for-the-visualization-and-analysis-of-nanopore-sequencing-data#item-annotation-3390 Wed, 23 May 2018 04:34:50 -0500 https://bioinformaticsonline.com/bookmarks/view/34396/pore-an-r-package-for-the-visualization-and-analysis-of-nanopore-sequencing-data#item-annotation-3390 <![CDATA[Comment by Rahul Nayak]]> We now need to install the poRe dependencies in R, which is very easy:


R
source("http://www.bioconductor.org/biocLite.R")
biocLite("rhdf5")
install.packages(c("shiny","bit64","data.table","svDialogs"))
q()

R may ask if you want to install into a local library, just say Y and accept defaults.  We need to download poRe from sourecforge and we are using version 0.16

Once downloaded, and back at the Linux command line:


R CMD INSTALL poRe_0.16.tar.gz

The fastq extraction scripts for poRe are in github, so let’s go get those:


git clone https://github.com/mw55309/poRe_scripts.git

We will assemble using SPAdes, so let’s go get that:


wget http://spades.bioinf.spbau.ru/release3.6.2/SPAdes-3.6.2-Linux.tar.gz
gunzip < SPAdes-3.6.2-Linux.tar.gz | tar xvf -

Now, we are ready to go.  First off, let’s extract the 2D sequence data as FASTQ from the MinION data.  Nick’s SQK-MAP-006 data are in the old FAST5 format so we use the script in “old_format”:


./poRe_scripts/old_format/extract2D MAP006-1/MAP006-1_downloads/pass/ > minion.pass.2D.fastq &
]]> Rahul Nayak