View source for SemiBin

[[Category:Software]]
{|<!--CONFIGURATION: REQUIRED-->
|{{#vardefine:app|SemiBin}}
|{{#vardefine:url|https://semibin.readthedocs.io/en/latest/}}
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
|{{#vardefine:conf|}}           <!--CONFIGURATION-->
|{{#vardefine:exe|semibin}}    <!--ADDITIONAL INFO-->
|{{#vardefine:job|}}            <!--JOB SCRIPTS-->
|{{#vardefine:policy|}}         <!--POLICY-->
|{{#vardefine:testing|}}       <!--PROFILING-->
|{{#vardefine:faq|}}             <!--FAQ-->
|{{#vardefine:citation|}}       <!--CITATION-->
|{{#vardefine:installation|}} <!--INSTALLATION-->
|}
<!--BODY-->
<!--Description-->
{{#if: {{#var: url}}|
{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}

DESCRIPTION

SemiBin is a command-line tool for metagenomic binning using deep learning. It handles both short and long reads and is designed to group metagenomic contigs into bins representing different organisms.

<!--Modules-->
==Environment Modules==
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.

==System Variables==
This module sets the following environment variables:
* HPC_SEMIBIN_DIR - installation directory
* HPC_SEMIBIN_BIN - executable directory

<!--Configuration-->
{{#if: {{#var: conf}}|==Configuration==
See the [[SemiBin_Configuration]] page for SemiBin configuration details.
|}}


<!--Job Scripts-->
{{#if: {{#var: job}}|==Job Script Examples==
See the [[SemiBin_Job_Scripts]] page for SemiBin job script examples.
|}}

<!--Policy-->
{{#if: {{#var: policy}}|==Usage Policy==

Please refer to the usage policy of SemiBin, including licensing and access details.

|}}

<!--Performance-->
{{#if: {{#var: testing}}|==Performance==

Performance testing results for SemiBin are available on the [[SemiBin_Performance]] page.

|}}

<!--Faq-->
{{#if: {{#var: faq}}|==FAQ==
*'''Q:''' **'''A:'''|}}

<!--Citation-->
{{#if: {{#var: citation}}|==Citation==
If you use this software in a publication please cite:

* Pan, S.; Zhu, C.; Zhao, X. M.; Coelho, L. P. A deep siamese neural network improves metagenome-assembled genomes in microbiome datasets across different environments. Nat Commun 13, 2326 (2022). [https://doi.org/10.1038/s41467-022-29843-y](https://doi.org/10.1038/s41467-022-29843-y)

* Pan, S., Zhao, X. M.; Coelho, L. P. SemiBin2: Self-Supervised Contrastive Learning Leads to Better MAGs for Short- and Long-Read Sequencing. Bioinformatics 39 (39 Suppl 1): i21–29. [https://doi.org/10.1093/bioinformatics/btad113](https://doi.org/10.1093/bioinformatics/btad113)
|}}

<!--Installation-->
{{#if: {{#var: installation}}|==Installation==
See the [[SemiBin_Install]] page for SemiBin installation notes.|}}

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