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Which NGS alignment algorithm has the smallest memory need?

Hi,

I was wondering which alignment algorithm has the smallest memory need. I am trying to make a cloud pipeline without using paralleisation at first. It would be for ~ 100 bp illumina reads. I have previously used BWA which I believe needs a minimum of 4 GB and I am now experimenting with Bowtie2 which appears to need more? How do the others i.e. bowtie compare?

Thanks,
Matt

alignment sequencing next-gen
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updated by Ram Ram • written by mattbawn • mattbawn

Human genome? Is speed or accuracy at all a concern? What are your goals (snps, indels, simple tag counts)?

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updated by Ram Ram • written by Sean Davis Sean Davis

Yes, Human Genome. No concerns regarding speed or accuracy at this stage and also just SNPs.

Thanks,

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updated by Ram Ram • written by mattbawn • mattbawn

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