Hi all,
I have Illumina HighSeq paired end reads and I'm looking for some strategy to apply a de novo assembly for it.
The inicial total number of reads in the two files was 240 Millions (The sum of files sizes: 56 GB). After the cleaning step, the total number of reads has been reduced to 81 Millions (21 GB).
I'm tring to assemble this data with the abyss-pe. This software work good with a small paired-end files. But when I run it on my data, even using 70GB of Ram the assembly don't finish and don't give results. I tested it with smal kmer (30) and big kmer (64), and also turned the minimum coverage to 40. No result.
Someone knows any strategy or pipeline to assemble a such large amount of illumina paired end data?
Thank you very much
I have Illumina HighSeq paired end reads and I'm looking for some strategy to apply a de novo assembly for it.
The inicial total number of reads in the two files was 240 Millions (The sum of files sizes: 56 GB). After the cleaning step, the total number of reads has been reduced to 81 Millions (21 GB).
I'm tring to assemble this data with the abyss-pe. This software work good with a small paired-end files. But when I run it on my data, even using 70GB of Ram the assembly don't finish and don't give results. I tested it with smal kmer (30) and big kmer (64), and also turned the minimum coverage to 40. No result.
Someone knows any strategy or pipeline to assemble a such large amount of illumina paired end data?
Thank you very much
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