Difference between revisions of "Bismark"
Jump to navigation
Jump to search
Moskalenko (talk | contribs) m (Text replace - "{{App_Description|app={{#var:app}}|url={{#var:url}}}}|}}" to "{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} ") |
Moskalenko (talk | contribs) m (Text replacement - "#uppercase" to "uc") |
||
(9 intermediate revisions by 2 users not shown) | |||
Line 1: | Line 1: | ||
− | [[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]][[Category:NGS]] | + | [[Category:Software]][[Category:Bioinformatics]][[Category:Genomics]][[Category:NGS]][[Category:Methylation]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|bismark}} | |{{#vardefine:app|bismark}} | ||
Line 13: | Line 13: | ||
|{{#vardefine:testing|}} <!--TESTING/PROFILING--> | |{{#vardefine:testing|}} <!--TESTING/PROFILING--> | ||
|{{#vardefine:faq|}} <!--FAQ--> | |{{#vardefine:faq|}} <!--FAQ--> | ||
− | |{{#vardefine:citation|}} <!--CITATION--> | + | |{{#vardefine:citation|1}} <!--CITATION--> |
|{{#vardefine:installation|}} <!--INSTALLATION--> | |{{#vardefine:installation|}} <!--INSTALLATION--> | ||
|} | |} | ||
Line 22: | Line 22: | ||
Bismark is a bisulfite read mapper and methylation caller. | Bismark is a bisulfite read mapper and methylation caller. | ||
− | + | ||
− | |||
− | |||
− | |||
− | |||
<!--Modules--> | <!--Modules--> | ||
− | + | ==Required Modules== | |
− | + | [[Modules|modules documentation]] | |
+ | ===Serial=== | ||
+ | *{{#var:app}} | ||
<!--Add additional HPC_FOO_BIN and other ENV VARIABLES below--> | <!--Add additional HPC_FOO_BIN and other ENV VARIABLES below--> | ||
+ | ==System Variables== | ||
+ | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory | ||
<!--Run--> | <!--Run--> | ||
+ | |||
{{#if: {{#var: exe}}|==How To Run== | {{#if: {{#var: exe}}|==How To Run== | ||
DOUBLE_CLICK_TO_WRITE_INSTRUCTIONS_ON_RUNNING_THE_ACTUAL_BINARY | DOUBLE_CLICK_TO_WRITE_INSTRUCTIONS_ON_RUNNING_THE_ACTUAL_BINARY | ||
Line 43: | Line 44: | ||
See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | See the [[{{PAGENAME}}_PBS]] page for {{#var: app}} PBS script examples.|}} | ||
<!--Policy--> | <!--Policy--> | ||
− | {{#if: {{#var: policy}}|==Usage | + | {{#if: {{#var: policy}}|==Usage Policy== |
WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used) | WRITE USAGE POLICY HERE (perhaps templates for a couple of main licensing schemes can be used) | ||
|}} | |}} | ||
Line 56: | Line 57: | ||
{{#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: | ||
− | + | ||
+ | Krueger F, Andrews SR. Bismark: a flexible aligner and methylation caller for | ||
+ | Bisulfite-Seq applications. Bioinformatics. 2011 Jun 1;27(11):1571-2. doi: | ||
+ | 10.1093/bioinformatics/btr167. Epub 2011 Apr 14. PubMed PMID: 21493656; PubMed | ||
+ | Central PMCID: PMC3102221. | ||
|}} | |}} | ||
<!--Installation--> | <!--Installation--> | ||
Line 62: | Line 67: | ||
See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}} | See the [[{{PAGENAME}}_Install]] page for {{#var: app}} installation notes.|}} | ||
__NOTOC____NOEDITSECTION__ | __NOTOC____NOEDITSECTION__ | ||
+ | =Validation= | ||
+ | * Validated 4/5/2018 |
Revision as of 21:01, 6 December 2019
Description
Bismark is a bisulfite read mapper and methylation caller.
Required Modules
Serial
- bismark
System Variables
- HPC_BISMARK_DIR - installation directory
Citation
If you publish research that uses bismark you have to cite it as follows:
Krueger F, Andrews SR. Bismark: a flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics. 2011 Jun 1;27(11):1571-2. doi: 10.1093/bioinformatics/btr167. Epub 2011 Apr 14. PubMed PMID: 21493656; PubMed Central PMCID: PMC3102221.
Validation
- Validated 4/5/2018