Difference between revisions of "Ngs-bits"
Jump to navigation
Jump to search
(Created page with "Category:SoftwareCategory:biologyCategory:sequencing {|<!--CONFIGURATION: REQUIRED--> |{{#vardefine:app|ngsbits}} |{{#vardefine:url|https://github.com/imgag/ngs-bi...") |
|||
| (2 intermediate revisions by 2 users not shown) | |||
| Line 1: | Line 1: | ||
| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:Sequencing]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|ngsbits}} | |{{#vardefine:app|ngsbits}} | ||
| Line 18: | Line 18: | ||
{{App_Description|app={{#var:app}}|url={{#var:url}}|name={{#var:app}}}}|}} | {{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--> | <!--Modules--> | ||
| Line 24: | Line 32: | ||
Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | Run <code>module spider {{#var:app}}</code> to find out what environment modules are available for this application. | ||
==System Variables== | ==System Variables== | ||
| − | * HPC_{{ | + | * HPC_{{uc:{{#var:app}}}}_DIR - installation directory |
<!--Configuration--> | <!--Configuration--> | ||
{{#if: {{#var: conf}}|==Configuration== | {{#if: {{#var: conf}}|==Configuration== | ||
Latest revision as of 16:57, 10 June 2022
Description
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.
Environment Modules
Run module spider ngsbits to find out what environment modules are available for this application.
System Variables
- HPC_NGSBITS_DIR - installation directory