Hello SEQ-users,
After working for some time on 454 16S microbiota analysis, I recently moved to Illumina and metagenomics. And the problems begin...
I have this dataset from an Illumina run. It has been cleaned (QC) of low quality bases and sequences by the BGI (which performed the actual sequencing). The result is a 35Gb file of 100 bp X 2 (paired ends) sequences. I want to analyse gene pathways and taxa and compare them with other samples.
The first suggestion I had to manipulate the data was to assemble the contigs. I tried Metavelvet and Spades, but to no avail so far. If I understand correctly the error output log, they are using to much memory. I am running them on the university cluster but apparently 24 Gb of RAM is not enough... And this is just a test run, we are supposed to receive anytime soon microbiota sequences from hundreds of patients...
Is there something wrong in my usage of the programs ?
Is there a better solution than assembly for this kind of data ?
Should I just move on to a more powerful environment ? If yes, which one ?
Any piece of information would be welcome at this point
After working for some time on 454 16S microbiota analysis, I recently moved to Illumina and metagenomics. And the problems begin...
I have this dataset from an Illumina run. It has been cleaned (QC) of low quality bases and sequences by the BGI (which performed the actual sequencing). The result is a 35Gb file of 100 bp X 2 (paired ends) sequences. I want to analyse gene pathways and taxa and compare them with other samples.
The first suggestion I had to manipulate the data was to assemble the contigs. I tried Metavelvet and Spades, but to no avail so far. If I understand correctly the error output log, they are using to much memory. I am running them on the university cluster but apparently 24 Gb of RAM is not enough... And this is just a test run, we are supposed to receive anytime soon microbiota sequences from hundreds of patients...
Is there something wrong in my usage of the programs ?
Is there a better solution than assembly for this kind of data ?
Should I just move on to a more powerful environment ? If yes, which one ?
Any piece of information would be welcome at this point
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