bowtie2-build --noauto parameter
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20 months ago
tea.vuki ▴ 20

Hi! I am trying to learn bowtie2 suite and I have a question regarding bowtie2-build. For the option --noauto it states:

Disable the default behavior whereby bowtie2-build automatically selects values for the --bmax, --dcv and --packed parameters according to available memory. Instead, user may specify values for those parameters. If memory is exhausted during indexing, an error message will be printed; it is up to the user to try new parameters.

However, when I use the command bowtie2-build --noauto path/to/file NAME, I get the same result as when I use it without --noauto option. Does this mean that I have to specify exact values for --bmax, --dcv and --packed at the same command? Meaning that my command line should look like: bowtie2-build --noauto --packed --dcv <int> --bmax <int> path/to/file NAME?

And, regarding that, is it possible to use the --bmax option for example without --noauto? For example, can I use bowtie2-build --bmax <int> path/to/file NAME? And in that case, what is the point of --noauto option?

bowtie2 • 560 views
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Does this mean that I have to specify exact values for --bmax, --dcv and --packed at the same command? Meaning that my command line should look like: bowtie2-build --noauto --packed --dcv <int> --bmax <int> path/to/file NAME?

If I read the documentation correctly, you can specify some or all of those params if you specify --noauto. In other words if you can specify just --bmax. --noauto exists to allow flexibility.

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Yes, thank you! I understand that, and I tested it extensively, however the part that I don't understand is why do I have to use --noauto when I get the exact same output with both --noauto --packed and only --packed command line.

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