PACVr

Plastome Assembly Coverage Visualization in R

INSTALLATION

library(devtools)
install_github("michaelgruenstaeudl/PACVr")

Note: Detailed installation instructions can be found in the package vignette.

PRE-FORMATTING INPUT

Due to the internal usage of R package genbankr, any GenBank flatfile must conform to the following specifications:

• Flatfile must include a source feature at start of feature table
• All exon features (plus their qualifier lines) must be removed: sed -i -e '/ exon/,+2d' input.gb
• All redundant complement specifications must be removed: sed -i -z 's/),\s*complement(/,/g' input.gb

USAGE

# In R:
library(PACVr)
gbkFile <- system.file("extdata", "NC_045072/NC_045072.gb", package="PACVr")
bamFile <- system.file("extdata", "NC_045072/NC_045072_PlastomeReadsOnly.sorted.bam", 
                       package="PACVr")
outFile <- paste(tempdir(), "/NC_045072_AssemblyCoverage_viz.pdf", sep="")
PACVr.complete(gbk.file=gbkFile, bam.file=bamFile, windowSize=250, 
               logScale=FALSE, threshold=0.5, syntenyLineType=3, 
               relative=TRUE, textSize=0.5,  verbose=FALSE, 
               output=outFile)

OUTPUT

FULLY AUTOMATED

SMPLNME="Cb01A_IOGA"
INFASTA=${SMPLNME}.fasta
READSR1=Cb01A_PlastomeReadsOnly_R1.fastq
READSR2=Cb01A_PlastomeReadsOnly_R2.fastq

mkdir -p db
bowtie2-build $INFASTA db/${SMPLNME}
bowtie2 -x db/${SMPLNME} -1 $READSR1 -2 $READSR2 -S ${SMPLNME}_mapping.sam
samtools view -Sb -F 0x04 ${SMPLNME}_mapping.sam > ${SMPLNME}_mapping_OneMoreLocations.bam
samtools sort ${SMPLNME}_mapping_OneMoreLocations.bam > ${SMPLNME}_mapping_OneMoreLocations.sorted.bam
rm $(ls *.?am | grep -v sorted)
samtools index ${SMPLNME}_mapping_OneMoreLocations.sorted.bam
Rscript PACVr/inst/extdata/PACVr_Rscript.R -k ${SMPLNME}.gb -b ${SMPLNME}_mapping_OneMoreLocations.sorted.bam -t 0.5 -r TRUE -d FALSE -o ${SMPLNME}_CoverageDepth.pdf

CITATION

Using PACVr in your research? Please cite it!

@article {GruenstaeudlAndJenke2020,
    author = {Gruenstaeudl, M. and Jenke, N.},
    title = {PACVr: plastome assembly coverage visualization in R},
    year = {2020},
    doi = {10.1186/s12859-020-3475-0},
    journal = {BMC Bioinformatics},
    volume = {21},
    pages = {207}
}

CHANGELOG

See CHANGELOG.md for a list of recent changes to the software.