Difference between revisions of "ESPRIT"
Moskalenko (talk | contribs) (Created page with "Category:SoftwareCategory:BioinformaticsCategory:NGSCategory:Metagenomics {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|esprit}} |{{#vardefine:url|http://...") |
Moskalenko (talk | contribs) |
||
| Line 10: | Line 10: | ||
|{{#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--> | ||
|} | |} | ||
| Line 54: | Line 54: | ||
{{#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. | ||
| + | |||
| + | ESPRIT ignores end gaps and uses affined gap penalties (i.e., continuous gaps are counted as one gap). | ||
|}} | |}} | ||
<!--PBS scripts--> | <!--PBS scripts--> | ||
| Line 73: | Line 75: | ||
{{#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: | ||
| − | + | ||
| + | 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. | ||
|}} | |}} | ||
<!--Installation--> | <!--Installation--> | ||
Revision as of 16:41, 18 December 2012
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.
Required Modules
Serial
- esprit
System Variables
- HPC_{{#uppercase:esprit}}_DIR
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.