Difference between revisions of "SPAdes"

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m (Text replacement - "#uppercase" to "uc")
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<!--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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{{#if: {{#var: exe}}|==Additional Information==
 
{{#if: {{#var: exe}}|==Additional Information==
  
WRITE_ADDITIONAL_INSTRUCTIONS_ON_RUNNING_THE_SOFTWARE_IF_NECESSARY
+
[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>
  
 
|}}
 
|}}

Revision as of 20:37, 27 May 2022

Description

spades website  

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

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

[trinity]
max_memory:8G
kmer_coverage:2

[spades]
max_memory:6G
cov_cutoff:5