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 email@example.com mailing list. You can contact me personally as well, but please open an issue first.
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.
GNU General Public License, version 2.
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
all the graphics parameters I added led to large numbers of arguments
to functions and high complexity. This rewrite uses
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
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
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
tool can do this; you can get it here
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