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454 gsAssemble (Newbler) memory requirements
How do memory requirements scale with number of bases (or reads) for assemblies of 454 data on Newbler? I'm looking at sequencing a 3 GB genome to 7-8X coverage and doing a de novo assembly.
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kbrad,
Are you sure you want to do a human size genome (3Gbp) using 454? To even get to 8X coverage on this would require ~50 runs. (That would be ~$500,000 US at most places.) And typically one needs to go up to 20 - 25X coverage for true de novo assembly using 454.
Aside from these considerations I seriously doubt gsAssembler (newbler) could handle anything even close to 3Gbp. -
Supposedly Assembler can handle up to 3Gbp genomes, as per their website. The manual says to contact your Roche rep if planning any assemblies >500Mbp.
I believe the memory requirement is 3bytes per read base, as per a Roche powerpoint from June 2009 (this may be different from the current version).Comment
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Roche 454's answer
I did learn from 454 tech support that 3 Gb genomes have been assembled with gsAssembler (Newbler) - including human. The memory requirements are 4 bytes per base to be assembled, so about 120 GB for 10x coverage of a 3 Gb genome.Comment
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