As the doctor gone rogue

June 21, 2013

How to install software or upgrade from old unsupported release? – Ask Ubuntu

Filed under: miscellaneous — Tags: , , — hypotheses @ 10:34 pm

I'm trying to install CNVWorkshop (cnv.chop.edu), but now facing problem of running Ubuntu 10.10 which has faced the end-of-life since April 2013. So, now running "sudo apt-get install" anything would not work, since the repo was set to look for files from archive.ubuntu.com.
AAfter spending sometimes 'google' as usual, here's where I end up.

Not that I intended not to upgrade to a newer release, but this is probably a relatively faster way to deploy another software that I still need to use.

sudo sed -i -e 's/archive.ubuntu.com\|security.ubuntu.com/old-releases.ubuntu.com/g' /etc/apt/sources.list
sudo apt-get update && sudo apt-get dist-upgrade

 

via How to install software or upgrade from old unsupported release? – Ask Ubuntu.

June 16, 2013

Ion Torrent PGM vs PacBio vs MiSeq

Filed under: genetics, NGS — hypotheses @ 1:05 am

“It’s a lot cheaper to buy PGM compared to other sequencing platform. So, should we buy it?”

A common concern regarding this question is whether the sequencing quality is alright? This is one of the first concern Ion Torrent seems to have experience since they first launched their first sequencer.

Quail, et al took a look at three platform in their paper. Although they have only looked at microbial genome with variable GC/AT content. They showed that there still seems to be a problem with Ion Torrent PGM platform when they sequence Plasmodium genome. Moreover, the false positive rate of base calling from Ion Torrent platform is still higher.

This data may not be applicable to human genome sequencing, but it deserves a closer look in my opinion.

BMC Genomics | Full text | A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers.

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