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Question: commonly used mapping mode parameters on lastz
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gravatar for kara.powder
16 months ago by
kara.powder • 0
United States
kara.powder • 0 wrote:

What are the specific parameters for all of the commonly used mapping modes in lastz? In other words, if I wanted to run the "Roche-454 75% identity" mode either using the full parameter list or on command line, what settings do I need to put in?
lastz parameters mapping mode • 314 views
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modified 16 months ago by Jennifer Hillman Jackson ♦ 25k • written 16 months ago by kara.powder • 0
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gravatar for Jennifer Hillman Jackson
16 months ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:

Hello,

From the lastz_wrapper.py script (this can be viewed in the Tool Shed or the repository itself, linked here).

    <when value="pre_set">
        <param name="pre_set_options" type="select" label="Select mapping mode">
            <option value="yasra98">Roche-454 98% identity</option>
            <option value="yasra95">Roche-454 95% identity</option>
            <option value="yasra90">Roche-454 90% identity</option>
            <option value="yasra85">Roche-454 85% identity</option>
            <option value="yasra75">Roche-454 75% identity</option>
            <option value="yasra95short">Illumina 95% identity</option>
            <option value="yasra85short">Illumina 85% identity</option>
        </param>

Lastz manual links:

Hope this helps! Jen, Galaxy team
ADD COMMENT • link written 16 months ago by Jennifer Hillman Jackson ♦ 25k
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