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README.md

qrqc - Quick Read Quality Control

qrqc and all supporting documentation Copyright (c) Vince Buffalo, 2011-2012

Contact: Vince Buffalo vsbuffaloAAAAA@gmail.com (with the poly-A tail removed)

If you wish to report a bug, please open an issue on Github (http://github.com/vsbuffalo/qrqc/issues) or send it to the bioconductor@r-project.org mailing list. You can contact me personally as well, but please open an issue first.

About

qrqc (short for "Quick Read Quality Control") is a fast and extensible package that reports basic quality and summary statistics on FASTQ and FASTA files, including base and quality distribution by position, sequence length distribution, and common sequences.

License

GNU General Public License, version 2.

FAQ

Why ggplot2?

I've had some feature requests for qrqc since its release, mostly related to customizing the graphics. Since data accessibility and custom graphics were the reason I created qrqc, I initially rewrote qrqc to provide more graphics options through lattice. However, all the graphics parameters I added led to large numbers of arguments to functions and high complexity. This rewrite uses ggplot2, which is a very excellent way to create graphics as any graphics object can be further manipulated.

Why do you use Monte Carlo simulations to generate the smooth curve?

qrqc is fast because it bins the quality scores of bases by positions; there is data summarization done by readSeqFile. To create a smooth curve, the function needs multiple data points (not binned data), which I simulate via Monte Carlo draws from the quality distribution by position. This is an approximation, but it leads to a smooth curve which can create a useful visual tool in assessing quality drops.

What do I do about bad quality regions?

Illumina reads often have poor 3'-end qualities. I've noticed that HiSeq machines also produce poor quality 5'-ends. For increased mapping rates and better assmeblies, it is generally advisable that these poor quality regions be trimmed off. Nik Joshi's took sickle tool can do this; you can get it here http://github.com/najoshi/sickle.

3'-end adapter contamination can be difficult to recognize (and thus remove) due to poor quality and likely incorrect bases. I've developed a tool called scythe that removes

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