Difference between revisions of "Bioinformatics Software"

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[[Category:Bio Informatics]]
 
[[Category:Bio Informatics]]
== Software installed in Bioinformatics cluster ==
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'''Software installed in Bioinformatics cluster'''
  
=== Bedtools ===
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= Bedtools =
 
Bedtools is a fast, flexible toolset for genome arithmetic.
 
Bedtools is a fast, flexible toolset for genome arithmetic.
  
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  module load bedtools
 
  module load bedtools
  
=== GATK ===
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= GATK =
 
Genome Analysis Toolkit. It is a collection of command-line tools for analyzing high-throughput sequencing data with a primary focus on variant discovery.  
 
Genome Analysis Toolkit. It is a collection of command-line tools for analyzing high-throughput sequencing data with a primary focus on variant discovery.  
  
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  module load gatk
 
  module load gatk
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= SourceTracker2 =
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SourceTracker is a Bayesian approach to estimate the proportion of contaminants in a given community that come from possible source environments.
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[https://github.com/biota/sourcetracker2 Webpage]
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Usage:
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module load conda-st2

Latest revision as of 15:03, 23 September 2019

Software installed in Bioinformatics cluster

Bedtools

Bedtools is a fast, flexible toolset for genome arithmetic.

Webpage

Installed version: 2.29.0

Usage:

module load bedtools

GATK

Genome Analysis Toolkit. It is a collection of command-line tools for analyzing high-throughput sequencing data with a primary focus on variant discovery.

The tools can be used individually or chained together into complete workflows.

Webpage

Installed version: 4.1.3.0

Usage:

module load gatk

SourceTracker2

SourceTracker is a Bayesian approach to estimate the proportion of contaminants in a given community that come from possible source environments.

Webpage

Usage:

module load conda-st2