View source for Graftm

[[Category:Software]][[Category:Phylogenetics]]
{|<!--CONFIGURATION: REQUIRED-->
|{{#vardefine:app|graftm}}
|{{#vardefine:url|https://github.com/geronimp/graftM}}
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GraftM is a tool for finding genes of interest in metagenomes, metatranscriptomes, and whole genomes. Using modular gene packages, GraftM will search the provided sequences using hmmsearch (HMMER) and place the identified sequences into a pre-constructed phylogenetic tree. The provides fast, phylogenetically informed community profiles and genome annotations.

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

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{{#if: {{#var: conf}}|==Configuration==
See the [[{{PAGENAME}}_Configuration]] page for {{#var: app}} configuration details.
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{{#if: {{#var: exe}}|==Additional Information==

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{{#if: {{#var: job}}|==Job Script Examples==
See the [[{{PAGENAME}}_Job_Scripts]] page for {{#var: app}} Job script examples.
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{{#if: {{#var: policy}}|==Usage Policy==

WRITE USAGE POLICY HERE (Licensing, usage, access).

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{{#if: {{#var: testing}}|==Performance==

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

[https://academic.oup.com/nar/article/46/10/e59/4942468 GraftM: a tool for scalable, phylogenetically informed classification of genes within metagenomes. Joel A Boyd Ben J Woodcroft Gene W Tyson Nucleic Acids Research, Volume 46, Issue 10, 1 June 2018, Pages e59, https://doi.org/10.1093/nar/gky174]

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{{#if: {{#var: installation}}|==Installation==
See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}}
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