Purpose
GenomicBreaks is a R package using Bioconductor libraries to analyse pairwise alignments of whole genomes in which the gene order has been scrambled by evolution, like in the picture below that represents the comparison of homologous chromosomes in two distantly related molds, N. crassa (chrIII) and P. comata (chr7).
This package is especially designed to parse and process the alignment files produced by the our pairwise genome alignment pipeline, but should be capable to import output of other pipelines as well.
Installation
Install the package.
If you have Bioconductor and the remotes already installed, the following should work.
Rscript -e 'remotes::install_github("oist/GenomicBreaks", repos=BiocManager::repositories())'Add dependencies=TRUE if you would like to install the packages needed to build the vignettes.
How to create a Singularity container with GenomicBreaks installed.
See the Singularity reciepe file
singularity build --fakeroot GenomicBreaks.sif Singularity.defGenomicBreaks in brief:
A pairwise alignment of two genomes is loaded in GBreaks objects wrapping the GRanges class. Here is an example:
GBreaks object with 505 ranges and 2 metadata columns:
seqnames ranges strand | score query
<Rle> <IRanges> <Rle> | <numeric> <GRanges>
[1] chrI 5860-10010 + | 10609 NC_047487.1:8723-12716
[2] chrI 11157-11782 + | 1253 NC_047487.1:13035-13680
[3] chrI 25371-26528 + | 3651 NC_047487.1:15380-16537
[4] chrI 26849-29699 + | 6130 NC_047487.1:17263-20175
[5] chrI 29937-30607 + | 767 NC_047487.1:20203-20866
... ... ... ... . ... ...
[501] chrM 67039-67870 + | 1441 NC_018044.1:7758-8439
[502] chrM 68205-68580 + | 830 NC_018044.1:8783-9180
[503] chrM 69178-76168 + | 14528 NC_018044.1:9650-16261
[504] chrM 77356-80022 + | 8066 NC_018044.1:53206-55865
[505] chrM 80919-85779 + | 6712 NC_018044.1:57885-61592
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seqinfo: 17 sequences (1 circular) from sacCer3 genomeSee “Get started” on https://oist.github.io/GenomicBreaks for further details.