Difference between revisions of "BRANCH"

Revision as of 14:10, 13 June 2022

Description

branch website
BRANCH is a software that extends de novo transfrags and identifies novel transfrags with DNA contigs or genes of close related species. BRANCH discovers novel exons first and then extends/joins fragmented de novo transfrags, so that the resulted transfrags are more complete.

Environment Modules

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

System Variables

HPC_BRANCH_DIR - installation directory

Citation

If you publish research that uses branch you have to cite it as follows: If you use BRANCH, please cite the following paper:

Bao E, Jiang T, Girke T (2013). BRANCH: boosting RNA-Seq assemblies with partial or related genomic sequences. Bioinformatics: epub.

@@ Line 19: / Line 19: @@
 BRANCH is a software that extends de novo transfrags and identifies novel transfrags with DNA contigs or genes of close related species. BRANCH discovers novel exons first and then extends/joins fragmented de novo transfrags, so that the resulted transfrags are more complete.
 <!--Modules-->
-==Required Modules==
+==Environment Modules==
-===Serial===
+Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application.
-* {{#var:app}}
-<!--
-===Parallel (OpenMP)===
-* intel
-* {{#var:app}}
-===Parallel (MPI)===
-* intel
-* openmpi
-* {{#var:app}}
--->
 ==System Variables==
-* HPC_{{uc:{{#var:app}}}}_DIR
+* HPC_{{uc:{{#var:app}}}}_DIR - installation directory
 <!--Configuration-->
 {{#if: {{#var: conf}}|==Configuration==
@@ Line 68: / Line 58: @@
 <!--Turn the Table of Contents and Edit paragraph links ON/OFF-->
 __NOTOC____NOEDITSECTION__
-=Validation=
-* Validated 4/5/2018