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
source("https://bioconductor.org/biocLite.R") biocLite("Rsamtools") biocLite("GenomicRanges") biocLite("IRanges")
Currently, qckitalign can be installed with
devtools by running:
RSeqAnto include searching for the
0x800flag in BAM files.
RSamtoolsand evaluate performance through
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