Difference between revisions of "SPAdes"

Latest revision as of 15:47, 22 August 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

@@ Line 1: / Line 1: @@
-[[Category:Software]][[Category:Biology]][[Category:Bioinformatics]][[Category:Software]]
+[[Category:Software]][[Category:Biology]][[Category:NGS]]
 {|<!--CONFIGURATION: REQUIRED-->
 |{{#vardefine:app|spades}}
@@ Line 5: / Line 5: @@
 <!--CONFIGURATION: OPTIONAL (|1}} means it's ON)-->
 |{{#vardefine:conf|}}           <!--CONFIGURATION-->
-|{{#vardefine:exe|}}            <!--ADDITIONAL INFO-->
+|{{#vardefine:exe|1}}            <!--ADDITIONAL INFO-->
 |{{#vardefine:job|}}            <!--JOB SCRIPTS-->
 |{{#vardefine:policy|}}         <!--POLICY-->
@@ Line 24: / Line 24: @@
 Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
 ==System Variables==
-* HPC_{{#uppercase:{{#var:app}}}}_DIR - installation directory
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
-* HPC_{{#uppercase:{{#var:app}}}}_BIN - executable directory
+* HPC_{{uc:{{#var:app}}}}_BIN - executable directory
 <!--Configuration-->
 {{#if: {{#var: conf}}|==Configuration==
@@ Line 33: / Line 33: @@
 {{#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>
 |}}