Jcvi 2016

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.