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BenLangmead / bowtie2

A fast and sensitive gapped read aligner
GNU General Public License v3.0
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Size of sam file #387

Closed cpavloud closed 10 months ago

cpavloud commented 2 years ago

It's not an issue, just a question.

I have as an input HiSeq paired end reads, around 500 GB in size (both of them). What size of .sam file should I expect? I have reached around 550 GB and it crashed because I exceeded my disk quota. So I need to know, more or less, how much more space I would need in order to ask the system administrators for it.

Thank you!

ch4rr0 commented 2 years ago

Hello,

It's not possible to predict the exact size of the SAM file, but it is not uncommon to see a 30-40% increase in file size.

ch4rr0 commented 2 years ago

You can also try streaming compression by piping the output to a compression tool, e.g.,

 ./bowtie2-align-s -x example/index/lambda_virus -1 example/reads/reads_1.fq -2 example/reads/reads_2.fq | gzip -o out.sam.gz