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Question: OLC based assemblers
2
gravatar for Abdul Rafay Khan
2.5 years ago by
Abdul Rafay Khan • 1000
Karachi, PK
Abdul Rafay Khan • 1000 wrote:

Looking for the OLC based assemblers to assembled Illumina large genome data. Already tried Celera but doesn't work.
ngs assembly • 1.2k views
ADD COMMENT • link •
modified 2.5 years ago by Brian Bushnell ♦ 16k • written 2.5 years ago by Abdul Rafay Khan • 1000
1
gravatar for Brian Bushnell
2.5 years ago by
Brian Bushnell ♦ 16k
Walnut Creek, USA
Brian Bushnell ♦ 16k wrote:

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.
ADD COMMENT • link modified 2.5 years ago • written 2.5 years ago by Brian Bushnell ♦ 16k
1

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

ADD REPLY • link written 2.5 years ago by Abdul Rafay Khan • 1000
1

Ahhh... sorry, it's here:

http://omega.omicsbio.org/

ADD REPLY • link written 2.5 years ago by Brian Bushnell ♦ 16k
1

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
ADD REPLY • link written 2.5 years ago by Abdul Rafay Khan • 1000
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