View source for Badread

[[Category:Software]][[Category:Phylogenetics]]
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|{{#vardefine:app|badread}}
|{{#vardefine:url|https://github.com/rrwick/Badread}}
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Badread is a long-read simulator tool that makes – you guessed it – bad reads! It can imitate many kinds of problems one might encounter in real long-read sets: chimeras, low-quality regions, systematic basecalling errors and more.

Badread does not try to be best at imitating real reads (though it's not too bad, see this comparison between Badread and other long-read simulators). Rather, it was intended to give users control over the quality of its simulated reads. I made Badread for the purpose of testing tools which take long reads as input. With it, one can increase the rate of different types of read problems, to see what effect it has.

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==Environment Modules==
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* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
* HPC_{{uc:{{#var:app}}}}_BIN - executable directory

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{{#if: {{#var: conf}}|==Configuration==
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{{#if: {{#var: exe}}|==Additional Information==

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{{#if: {{#var: policy}}|==Usage Policy==

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{{#if: {{#var: faq}}|==FAQ==
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{{#if: {{#var: citation}}|==Citation==
If you publish research that uses {{#var:app}} you have to cite it as follows:

[https://joss.theoj.org/papers/10.21105/joss.01316 Wick RR. Badread: simulation of error-prone long reads. Journal of Open Source Software. 2019;4(36):1316. doi:10.21105/joss.01316.]

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{{#if: {{#var: installation}}|==Installation==
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