Bioinformatics and genomics

Spring 2014
Lab 2
Feb 9th 2014

What we will do today
Run a De novo assembly of e.coli genome.
Calculate N50 values .
gsAssembler
How to run gsAssembler in GUI mode (and access ALGAE in terminal mode):

On PC: Start PuTTY, login as above, make sure host name and port number are
correct (and X11 is enabled) and Xming is running
In PuTTY type in gsAssembler, the GUI should open up

From a Mac:
1. Open up a terminal session, then type in the following command:
ssh -p 4410 -Y <your Net ID>@192.168.194.72

2. Enter your password
3. Type in gsAssembler

Launch a new project.
Select your read from Share folder, which is
R_2012_08_30_08_04_00_user_SN2-2ecoli-
92712_ecoli-92712.fastq
Go to Parameter tab, select Computation,
specify number of cores between 1-3 ( 0 = all
available cores, do not use this option)
Run the project using the default parameters
for minimum length and identity.




De novo assembly
N50 calculations
When the run is done go to results files and search for a
454contigGraph file.
Open the file in excel.









Go to your NYU classes website and download the excel
template for N50 calculation.
Copy the contig length from the first excel file and paste them
in the template and determine your N50.

Lab assignment
Repeat the assembly and the calculation for
the parameters below:
Increased minimum length to 60
Increased identity to 98%
Increased minimum length and identity ( 60 &
98%)
Compare the N50 values for the four runs.