QCKitalign, part of the QCKit suite by the Computational Biology Core at Brown, is a quality control package in R for reference genome read mapping alignment statistics in the SAM/BAM file format. SAM/BAM files are the de facto standard file format for storing NGS reads aligned to reference genomes. You can read more about them here. This package provides the following metrics:
qckitalign
has a lot of dependencies on Bioconductor packages. The commands to install them are below, and need to be run once before in order to properly install and run qckitalign
.
source("https://bioconductor.org/biocLite.R")
biocLite("Rsamtools")
biocLite("GenomicRanges")
biocLite("IRanges")
Currently, qckitalign can be installed with devtools
by running:
devtools::install_github("compbiocore/qckitalign",build_vignettes=TRUE)
library(qckitalign)
RSeqAn
to include searching for the 0x800
flag in BAM files.RSeqAn
instead of RSamtools
and evaluate performance through rbenchmark
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