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Old 02-25-2013, 05:53 AM   #1
raindancedani
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Location: USA

Join Date: Feb 2013
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Unhappy Soapdenovo stops at reading reads

Hi everyone,

I have 1 billion reads from Illumina GA and have been trying to run an assembly for a 0.8 Gb genome using Soapdenovo v 1.05. At some point during the reading process, the assembler stops running. All I can see in the log is that only some lanes were read. I have tried running only some of the reads, but it's been hard to understand if the problem is volume, reads headers, or any of the libraries.
Any help or suggestion will be greatly appreciated!

raindancedani*
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Old 03-16-2013, 01:22 PM   #2
Blahah404
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Try using some tool to clean the reads. I've seen soapdenovo crashing without explanation when the reads contain Ns (although sometimes it doesn't). I use the ALLPATHS-LG ErrorCorrectReads.pl script first to remove low quality reads, then follow it with khmer to get rid of redundant reads. That massively reduces the assembly time and complexity, and generally stops soapdenovo crashing.
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