OLC based assemblers

Question

[Abdul Rafay Khan]

Looking for the OLC based assemblers to assembled Illumina large genome data. Already tried Celera but doesn't work.

Answer 1

[Brian Bushnell]

There's also Newbler and Omega. Omega is intended for large genomes. Unfortunately, the current version does not appear to be available for download yet... but the older version, 1.0.2, is available.

[Abdul Rafay Khan]

can i have a link of Omega version 1.0.2? I am unable to find it

[Brian Bushnell]

Ahhh... sorry, it's here:

http://omega.omicsbio.org/

[Abdul Rafay Khan]

Trim my data using Sickle tool

Then run omega assembler

omega -pe ERR1_trim.fastq,ERR2_trim.fastq -l 60

13 minutes after running the command it stops and shows this

Currently in file: ../OverlapGraph.cpp Function: saveGraphToFile()
Function saveGraphToFile() finished in 16.359 Seconds.

Currently in file: ../OverlapGraph.cpp Function: calculateFlow()
Calling CS2

line 1 of input - it is not a Min-cost problem line
Command exited with non-zero status 1