PACVr-package: Plastome Assembly Coverage Visualization in R
In PACVr: Plastome Assembly Coverage Visualization
Description
Note
Author(s)
References
Description
PACVr visualizes the coverage depth of a complete plastid genome as well as the equality of its inverted repeat regions in relation to the circular, quadripartite genome structure and the location of individual genes.
Note
Input Requirements
The input to PACVr consists of two input files that contain information on (a) genome sequence and structure, and (b) on coverage depth. Specifically, users must provide (a) a file in GenBank flat file format that complies with the GenBank record specifications (https://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html), and (b) a file in BAM format that complies with the specifications described in the Sequence Alignment/Map Format documentation (https://samtools.github.io/hts-specs/SAMv1.pdf) and is accompanied by an ancillary index file.
Data Requirements
The user-supplied GenBank flat file must contain a sequence record of a complete plastid genome. For effective visualizations, the sequence record should contain a sequence feature for each of the inverted repeat regions, whereby the regions should be named 'IRa' and 'IRb' or 'Inverted Repeat a' and 'Inverted Repeat b', respectively. For effective visualizations, the total sequence length of the complete genome should be between 50 kb and 250 kb.
Author(s)
Michael Gruenstaeudl, Nils Jenke
Maintainer: Michael Gruenstaeudl m.gruenstaeudl@fu-berlin.de
References
Gruenstaeudl, M. and Jenke, N. (2019). PACVr: Plastome Assembly Coverage Visualization in R. bioRxiv 697821; doi: https://doi.org/10.1101/697821
PACVr documentation built on Nov. 23, 2020, 1:07 a.m.
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Description Note Author(s) References
Description
PACVr visualizes the coverage depth of a complete plastid genome as well as the equality of its inverted repeat regions in relation to the circular, quadripartite genome structure and the location of individual genes.
Note
Input Requirements
The input to PACVr consists of two input files that contain information on (a) genome sequence and structure, and (b) on coverage depth. Specifically, users must provide (a) a file in GenBank flat file format that complies with the GenBank record specifications (https://www.ncbi.nlm.nih.gov/Sitemap/samplerecord.html), and (b) a file in BAM format that complies with the specifications described in the Sequence Alignment/Map Format documentation (https://samtools.github.io/hts-specs/SAMv1.pdf) and is accompanied by an ancillary index file.
Data Requirements
The user-supplied GenBank flat file must contain a sequence record of a complete plastid genome. For effective visualizations, the sequence record should contain a sequence feature for each of the inverted repeat regions, whereby the regions should be named 'IRa' and 'IRb' or 'Inverted Repeat a' and 'Inverted Repeat b', respectively. For effective visualizations, the total sequence length of the complete genome should be between 50 kb and 250 kb.
Author(s)
Michael Gruenstaeudl, Nils Jenke
Maintainer: Michael Gruenstaeudl m.gruenstaeudl@fu-berlin.de
References
Gruenstaeudl, M. and Jenke, N. (2019). PACVr: Plastome Assembly Coverage Visualization in R. bioRxiv 697821; doi: https://doi.org/10.1101/697821
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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