Difference between revisions of "Ngs-bits"
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| − | [[Category:Software]][[Category: | + | [[Category:Software]][[Category:Biology]][[Category:Sequencing]] |
{|<!--CONFIGURATION: REQUIRED--> | {|<!--CONFIGURATION: REQUIRED--> | ||
|{{#vardefine:app|ngsbits}} | |{{#vardefine:app|ngsbits}} | ||
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{{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--> | ||
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