Difference between revisions of "Bioinformatics Software"
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[[Category:Bio Informatics]] | [[Category:Bio Informatics]] | ||
| − | + | '''Software installed in Bioinformatics cluster''' | |
| − | + | = Bedtools = | |
Bedtools is a fast, flexible toolset for genome arithmetic. | Bedtools is a fast, flexible toolset for genome arithmetic. | ||
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Installed version: 2.29.0 | Installed version: 2.29.0 | ||
| − | Usage: module load bedtools | + | 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. | ||
| + | |||
| + | [https://software.broadinstitute.org/gatk/documentation/ 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. | ||
| + | |||
| + | [https://github.com/biota/sourcetracker2 Webpage] | ||
| + | |||
| + | Usage: | ||
| + | |||
| + | 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.
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.
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.
Usage:
module load conda-st2
