Which NGS alignment algorithm has the smallest memory need?

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9.5 years ago

mattbawn ▴ 60

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 • 1.6k views

ADD COMMENT • link updated 3.1 years ago by Ram 43k • written 9.5 years ago by mattbawn ▴ 60

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

ADD REPLY • link updated 3.1 years ago by Ram 43k • written 9.5 years ago by Sean Davis 26k

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

Thanks,

ADD REPLY • link updated 3.1 years ago by Ram 43k • written 9.5 years ago by mattbawn ▴ 60

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