Is it possible to assemble a eukaryotic transcriptome from 50M Illumina paired end reads (101bp) using a machine with only 12 GB of RAM or am I going to have to find a bigger server? I've tried using Trinity, which can't manage it, but is there a more computationaly economical program I could use?
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12GB is a tiny amount of RAM for an assembly. I would recommend getting more if you can.
Otherwise, you could try Oases. I've had cases where assembly requires more RAM on Trinity than on Oases and vice versa.
Besides that you could try removing poor quality reads, duplicate reads, or overlapping reads. Just be sure that the remaining reads are still paired in the fastq files.
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With that few of reads you *might* be able to manage it will ABySS/Trans-ABySS. I'd suggest doing some quality trimming (Q=20 is usually reasonable) and excluding unique kmers to decrease your memory footprint. But with a modern desktop computer you should really be able to get up to 32 GB of RAM for pretty cheap. If you do this much its worth the extra $100-200.
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