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Welcome to the jcvi wiki! To use jcvi as a generic Bioinformatics library, please follow the instructions on the project page. This wiki hosts standalone applications within the library that are capable of solving domain-specific problems.

Applications

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

MCscan facilitates pairwise and multiple genome syntenic comparisons and visualizations.

Case studies

Genome build quality control

A suite of tools including genome size survey, genetic map and Hi-C heatmap to check for quality of genome build.

Breeding and genome diversity

A suite of tools including pedigree analysis and CNV between varieties.

Miscellaneus plotting

A suite of visualization routines in the package that might be useful to create customized plots.

FAQ

Plotting failed with error message "No such file or directory: 'latex'"

Please take a look at Get LaTeX for various options for each major OS. For example, on Debian-like Linux OS you can often do:

sudo apt-get install -y texlive texlive-latex-extra texlive-latex-recommended