Difference between revisions of "Bioinformatics Software"
From CsWiki
(2 intermediate revisions by the same user not shown) | |||
Line 1: | Line 1: | ||
[[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. | ||
Line 9: | Line 9: | ||
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