Difference between revisions of "SPAdes"
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(Created page with "Category:SoftwareCategory:BiologyCategory:BioinformaticsCategory:Software {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|spades}} |{{#vardefine:url|http://...") |
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| − | [[Category:Software]][[Category:Biology]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:NGS]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|spades}} | |{{#vardefine:app|spades}} | ||
| Line 5: | Line 5: | ||
<!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)--> | ||
|{{#vardefine:conf|}} <!--CONFIGURATION--> | |{{#vardefine:conf|}} <!--CONFIGURATION--> | ||
| − | |{{#vardefine:exe|}} <!--ADDITIONAL INFO--> | + | |{{#vardefine:exe|1}} <!--ADDITIONAL INFO--> |
|{{#vardefine:job|}} <!--JOB SCRIPTS--> | |{{#vardefine:job|}} <!--JOB SCRIPTS--> | ||
|{{#vardefine:policy|}} <!--POLICY--> | |{{#vardefine:policy|}} <!--POLICY--> | ||
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Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | ||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_BIN - executable directory |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
| Line 33: | Line 33: | ||
{{#if: {{#var: exe}}|==Additional Information== | {{#if: {{#var: exe}}|==Additional Information== | ||
| − | + | [https://cab.spbu.ru/files/release3.15.3/manual.html Spades Manual] | |
| + | |||
| + | You can create a personal phyluce config in ~/.phyluce.conf. It's mostly used to set trinity or spades memory with something like | ||
| + | <pre> | ||
| + | [trinity] | ||
| + | max_memory:8G | ||
| + | kmer_coverage:2 | ||
| + | |||
| + | [spades] | ||
| + | max_memory:6G | ||
| + | cov_cutoff:5 | ||
| + | </pre> | ||
|}} | |}} | ||
Latest revision as of 15:47, 22 August 2022
Description
St. Petersburg genome assembler
Environment Modules
Run module spider spades to find out what environment modules are available for this application.
System Variables
- HPC_SPADES_DIR - installation directory
- HPC_SPADES_BIN - executable directory
Additional Information
You can create a personal phyluce config in ~/.phyluce.conf. It's mostly used to set trinity or spades memory with something like
[trinity] max_memory:8G kmer_coverage:2 [spades] max_memory:6G cov_cutoff:5