Difference between revisions of "Ngs-bits"

Revision as of 18:10, 27 May 2022

Short-read sequencing tools.

Main tools

SeqPurge - A highly-sensitive adapter trimmer for paired-end short-read data (paper, poster from ECCB 2016 with more recent benchmarks).
SampleCorrelation - Calculates the variant overlap and correlation of two VCF/BAM files.
SampleGender - Determines sample gender based on a BAM file.
PERsim - Paired-end read simulator for Illumina reads.
CnvHunter - CNV detection from targeted resequencing data using non-matched control samples.

@@ Line 1: / Line 1: @@
-[[Category:Software]][[Category:biology]][[Category:sequencing]]
+[[Category:Software]][[Category:Biology]][[Category:Sequencing]]
 {|<!--CONFIGURATION: REQUIRED-->
 |{{#vardefine:app|ngsbits}}
@@ Line 18: / Line 18: @@
 {{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}}
-Short-read sequencing tools
+Short-read sequencing tools.
+Main tools
+* SeqPurge - A highly-sensitive adapter trimmer for paired-end short-read data (paper, poster from ECCB 2016 with more recent benchmarks).
+* SampleCorrelation - Calculates the variant overlap and correlation of two VCF/BAM files.
+* SampleGender - Determines sample gender based on a BAM file.
+* PERsim - Paired-end read simulator for Illumina reads.
+* CnvHunter - CNV detection from targeted resequencing data using non-matched control samples.
 <!--Modules-->
-==Environment Modules==
+==Required 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_{{uc:{{#var:app}}}}_DIR - installation directory