README.md

In compbiocore/qckitalign: Quality Control for Mapped Reads

qckitalign

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:

1. Chimeric reads, i.e. the proportion of sequencing reads that align to two distinct portions of the genome with less than x (by default 0) base pairs overlap.

Installation

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)

Future Improvements

• Use RSeqAn to include searching for the 0x800 flag in BAM files.
• Read a BAM file with RSeqAn instead of RSamtools and evaluate performance through rbenchmark.

compbiocore/qckitalign documentation built on May 21, 2019, 9:48 a.m.