BOL

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 &