Difference between revisions of "Jcvi 2016"
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Jcvi is a collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics. | Jcvi is a collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics. | ||
Jcvi comes with three applications which are | Jcvi comes with three applications which are described below: | ||
*ALLMAPS | *ALLMAPS | ||
ALLMAPS anchors genomic scaffolds onto linkage groups to reconstruct chromosomal assemblies. | ALLMAPS anchors genomic scaffolds onto linkage groups to reconstruct chromosomal assemblies. | ||
*GRABSEEDS | *GRABSEEDS | ||
GRABSEEDS facilitates computerized extraction of object features and text labels from digital images in large phenotyping experiments. | GRABSEEDS facilitates computerized extraction of object features and text labels from digital images in large phenotyping experiments. | ||
*MCscan (Python version) | *MCscan (Python version) | ||
Latest revision as of 12:26, 26 July 2018
Introduction
Jcvi is a collection of Python libraries to parse bioinformatics files, or perform computation related to assembly, annotation, and comparative genomics.
Jcvi comes with three applications which are described below:
- ALLMAPS
ALLMAPS anchors genomic scaffolds onto linkage groups to reconstruct chromosomal assemblies.
- GRABSEEDS
GRABSEEDS facilitates computerized extraction of object features and text labels from digital images in large phenotyping experiments.
- MCscan (Python version)
MCscan facilitates pairwise and multiple genome syntenic comparisons and visualizations.
Installed Version
The following version of jcvi is currently installed on the cluster:
jcvi/0.8.4-intel-2018a-Python-2.7.14
It is installed on the environment hpc-env/6.4.
Using jcvi
If you want to use jcvi you have to change the environment at first before loading the module.
module load hpc-env/6.4
module load jcvi
Now you have access to all functionalities and applications that jcvi offers.
If you want to know in detail, how to use the different programs, you might want to look up the jcvi wiki pages.
