Question: OLC based assemblers
2
gravatar for Abdul Rafay Khan
2.5 years ago by
Karachi, PK
Abdul Rafay Khan1000 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 COMMENTlink modified 2.5 years ago by Brian Bushnell16k • written 2.5 years ago by Abdul Rafay Khan1000
1
gravatar for Brian Bushnell
2.5 years ago by
Walnut Creek, USA
Brian Bushnell16k 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 COMMENTlink modified 2.5 years ago • written 2.5 years ago by Brian Bushnell16k
1

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

ADD REPLYlink written 2.5 years ago by Abdul Rafay Khan1000
1

Ahhh... sorry, it's here:

http://omega.omicsbio.org/

ADD REPLYlink written 2.5 years ago by Brian Bushnell16k
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 REPLYlink written 2.5 years ago by Abdul Rafay Khan1000
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 666 users visited in the last hour