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Old 02-27-2015, 08:46 AM   #1
Location: Fargo

Join Date: Dec 2011
Posts: 66
Default best assembler for 160PE and 100PE reads

Hi all,
I have about 60X combined coverage of my genome, but half of my reads are 100 base paired end reads and the other half is 160 base paired end reads. Any suggestions for which assembler would be the best one to use for a combined file of both read sets?

I have removed the high and low kmer read sets (since I really am primarily interested in single and low-copy regions of my genome) and total I have about 20GB of sequence for each end. I ran the Trinity Kmer reduction program (max of 30 X coverage/kmer) on my PE100 file and only reduced it from about 8GB to 5GB per end. This is about what I would have expected given my initial kmer selection scheme. The attempt to do this with the PE160 files failed for an unknown reason, but I would expect it to also would give me about a 40% reduction. Thus, I could probably -with some effort, get my combined files down to about 12Gb each before attempting the assembly.

Any advice about the best assembler or other strategies to assist in assembling my low-copy genome space (which should contain the bulk of my genes) is welcome.
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