Difference between revisions of "PBJelly"

Latest revision as of 17:07, 21 August 2022

Description

PBJelly is a highly automated pipeline that aligns long sequencing reads (such a PacBio RS reads or long 454 reads in fasta format) to high-confidence draft assembles. PBJelly fills or reduces as many captured gaps as possible to produce upgraded draft genomes. Each step in PBJelly's workflow can be run on a cluster, thus parallelizing the gap filling process for rapid turn around, even for very large eukaryotic genomes.

Environment Modules

Run module spider PBJelly to find out what environment modules are available for this application.

System Variables

HPC_PBJELLY_DIR - installation directory
HPC_PBJELLY_BIN
HPC_PBJELLY_CONF
HPC_PBJELLY_TEST

Additional Information

This module includes the full PBSuite.

@@ Line 1: / Line 1: @@
-[[Category:Software]][[Category:Biology]][[Category:Bioinformatics]]
+[[Category:Software]][[Category:Biology]][[Category:NGS]]
 {|<!--CONFIGURATION: REQUIRED-->
 |{{#vardefine:app|PBJelly}}
@@ Line 26: / Line 26: @@
 <!--Modules-->
-==Required Modules==
+==Environment Modules==
+Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
-===Serial===
-* {{#var:app}}
-<!--===Parallel (OpenMP)===
-* intel
-* {{#var:app}}
-===Parallel (MPI)===
-* intel
-* openmpi
-* {{#var:app}}
--->
 ==System Variables==
-* HPC_{{#uppercase:{{#var:app}}}}_DIR
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
-* HPC_{{#uppercase:{{#var:app}}}}_BIN
+* HPC_{{uc:{{#var:app}}}}_BIN
-* HPC_{{#uppercase:{{#var:app}}}}_CONF
+* HPC_{{uc:{{#var:app}}}}_CONF
-* HPC_{{#uppercase:{{#var:app}}}}_TEST
+* HPC_{{uc:{{#var:app}}}}_TEST
 <!--Configuration-->
 {{#if: {{#var: conf}}|==Configuration==
@@ Line 76: / Line 66: @@
 <!--Turn the Table of Contents and Edit paragraph links ON/OFF-->
 __NOTOC____NOEDITSECTION__
-=Validation=
-* Validate 4/5/2018