Question: How to index a large fasta file (>100GB) by using bowtie2-build
0
gravatar for taylor
29 days ago by
taylor0
taylor0 wrote:

I am wondering how to index a very large fasta file (~100GB) by using bowtie2-build? I have enlarged my memory up to 512G and use the parameter "--bmax 3 --dcv 4096" to minimize the memory usage, but it still failed...

So is there any possible solution to solve this problem? Thanks~

Here is the error message:

Using parameters --bmax 3 --dcv 4096

Doing ahead-of-time memory usage test

Ran out of memory; automatically trying more memory-economical parameters.

Total time for call to driver() for forward index: 01:17:56

Thanks,

index bowtie alignment genome • 146 views
ADD COMMENTlink modified 29 days ago by WouterDeCoster40k • written 29 days ago by taylor0
1

Centrifuge also can be useful https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5131823/

ADD REPLYlink written 28 days ago by grant.hovhannisyan1.7k

Are you sure bowtie is the right tool for the job? Which index are you building?

ADD REPLYlink written 29 days ago by WouterDeCoster40k

They are some environment microbes... I think bowtie is easy to use. Do you have some software recommended for this job? Thanks,

ADD REPLYlink written 29 days ago by taylor0
1

Those microbes may have highly similar sequences, making alignment erroneous. Take a look at kraken2 for species classification

ADD REPLYlink written 28 days ago by WouterDeCoster40k

OK. Thanks. I will try.

ADD REPLYlink written 28 days ago by taylor0

Maybe you could try bwa mem ? what do you want to do with the index ? which type of data ? which type of organism are you studying ?

ADD REPLYlink written 29 days ago by Nicolas Rosewick8.1k
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