Difference between revisions of "ESPRIT"
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| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]] |
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|{{#vardefine:testing|}} <!--PROFILING--> | |{{#vardefine:testing|}} <!--PROFILING--> | ||
|{{#vardefine:faq|}} <!--FAQ--> | |{{#vardefine:faq|}} <!--FAQ--> | ||
| − | |{{#vardefine:citation|}} <!--CITATION--> | + | |{{#vardefine:citation|1}} <!--CITATION--> |
|{{#vardefine:installation|}} <!--INSTALLATION--> | |{{#vardefine:installation|}} <!--INSTALLATION--> | ||
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of thousands of sequences within one day. | of thousands of sequences within one day. | ||
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| − | == | + | ==Environment Modules== |
| − | + | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | |
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==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
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{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
Several versions of the esprit_pc and hcluster binaries are available. The default version had the linked table size increased from 10 thousand to 100 thousand to handle larger numbers of sequences. There are also esprit_pc-1m, esprit_pc-10m, hcluster-1m, and hcluster-10m binaries with link table sizes of 1 and 10 million respectively. | Several versions of the esprit_pc and hcluster binaries are available. The default version had the linked table size increased from 10 thousand to 100 thousand to handle larger numbers of sequences. There are also esprit_pc-1m, esprit_pc-10m, hcluster-1m, and hcluster-10m binaries with link table sizes of 1 and 10 million respectively. | ||
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| + | ESPRIT ignores end gaps and uses affined gap penalties (i.e., continuous gaps are counted as one gap). | ||
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{{#if: {{#var: citation}}|==Citation== | {{#if: {{#var: citation}}|==Citation== | ||
If you publish research that uses {{#var:app}} you have to cite it as follows: | If you publish research that uses {{#var:app}} you have to cite it as follows: | ||
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| + | Y. Sun*, Y. Cai*, L. Liu, F. Yu, M. L. Farrell, W. McKendree, and W. Farmerie, (*equal contribution) ESPRIT: Estimating Species Richness Using Large Collections of 16S rRNA Pyrosequences, Nucleic Acids Research, vol. 37, no. 10, e76, 2009. | ||
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Latest revision as of 15:10, 15 August 2022
Description
Recent metagenomics studies of environmental samples suggest that microbial communities are much more diverse than previously reported, and deep sequencing will significantly increase the estimate of total species diversity. Massively parallel pyrosequencing technology enables ultra-deep sequencing of complex microbial populations rapidly and inexpensively. However, classifying large collections of 16S ribosomal sequences poses a serious computational challenge for existing algorithms. We proposed a new algorithm, referred to as ESPRIT, which addresses several computational limitations of prior methods. We developed two versions of ESPRIT, one for personal computers and one for computer clusters. The personal-computer version is used for small and medium-scale datasets and can process several tens of thousands sequences within a few minutes, while the computer-cluster version is for large-scale problems and is able to analyze several hundreds of thousands of sequences within one day.
Environment Modules
Run module spider esprit to find out what environment modules are available for this application.
System Variables
- HPC_ESPRIT_DIR - installation directory
Citation
If you publish research that uses esprit you have to cite it as follows:
Y. Sun*, Y. Cai*, L. Liu, F. Yu, M. L. Farrell, W. McKendree, and W. Farmerie, (*equal contribution) ESPRIT: Estimating Species Richness Using Large Collections of 16S rRNA Pyrosequences, Nucleic Acids Research, vol. 37, no. 10, e76, 2009.