Thursday, 3 September 2015

The Workflow | Ion S5 Next Generation Sequencing System







Thermo Fisher Scientific recently announced their new sequencer, the Ion S5™ Sequencer. The system was designed to free up researchers time with a simple load and go reagents and fast sequencing times. In the video below, you will see how simple the Ion S5 System is to setup. First, the video walks through initialization, a quick 30 minute process that gets the system ready for sequencing. Then, you just simply need to swap out the old chip used for initialization with the chip with your sample, loaded during an Ion Chef™ System run. And as far as speed on the Ion S5 System is concerned, sequencing is fast – allowing you to complete a run in as little as two hour thanks to the semiconductor sequencing technology.


Kevin: Hmmm why choose S5 for a model name .. don't you know about http://www.samsung.com/sg/galaxys5/ ?

Monday, 8 June 2015

Careers with Lee Kong Chian School of Medicine

Helping a friend
Look for a Postdoctoral Research Fellow in the Laboratory of Assistant Professor Xueli Guan http://jobs.jobstreet.com/sg/jobs/4568249?fr=30

Research Assistant
http://jobs.jobstreet.com/sg/jobs/4566463?fr=30

Saturday, 4 April 2015

four mistakes to avoid if you are analyzing data: useful reminder!

I have been following plotly for a while ... haven't had public data that I can play with on this though ... anyway they have a blog post that is a compilation of the 4 deadly sins of data analysis. Do check it out!

http://blog.plot.ly/post/113557928802/four-mistakes-to-avoid-if-youre-analyzing-data

Saturday, 15 November 2014

What 5G mobile networks portends for the future of personal genomics

ok I saw this a while back (a month ago, yes I have been busy) http://www.engadget.com/2014/10/14/samsung-5g-network-tests-oh-god-the-speed/

I am already very impressed with 4G (LTE) speeds but with 5G you can possibly achieve 150 mb/s to 940 mb/s which is mind blowing ...

Considering that you could then possibly upload via your mobile devices, your own 100 Gb bam file in about 10 seconds (sorry I wasn't thinking how much faster a youtube video would stream). Now Google is saying that they can store your genome (actually they meant your 30x WGS bam file) for $25 a year. But with 5G speeds, why would I even bother with that?

Heck, maybe in the future with an USB OTG cable connected to Oxford Nanopore's MinION your android phone will be able to sequence and upload in realtime your DNA obtained from a buccal swab. The cloud will have the fastq reads aligned and call variants instantaneously and download the 100 Gb bam to your microsd card.

Possible applications:

  1. Maybe in the future other than asking if you have a drug allergy, pharmacists will request to 'scan' your DNA for the most efficient drug. 
  2. another possible application might be having your DNA be your own personal identity card, 
  3. more routine sequencing of the human microbiome to monitor your health in relation to the gut microflora or other sites.


I am keen to find out what you think you can do if you could carry your whole genome sequencing with you and upload via mobile networks. Drop in your comments please!

Saturday, 13 September 2014

Wednesday, 27 August 2014

tabix and VCF file size limits

Today I learn that tabix can index bgzipped VCF files of 4 TB (compressed) and possibly bigger.... Mind blown ...

Source: Samtools-help mailing list
https://lists.sourceforge.net/lists/listinfo/samtools-help

Friday, 2 May 2014

Datanami, Woe be me