Shadow Regression

R package:

R code to try test data: test.R
Expect 30-60 minutes of run time on test data provided, depending on system.

Test data: SRR037452.fastq.rcnts.gz
This is one of the MAQC samples. More information can be found from the Short Read Archive.

PhiX genome in fasta format: phix.fasta

6/28/2013: Requires ShortRead version 1.18 or above. Earlier versions may cause problems in function getReadCnts().
5/14/2013: Package rebuilt to be compatible with R 3.0.
5/11/2012: Package released.

Please cite:
Wang, X. V., Blades, N., Ding, J., Sultana, R., & Parmigiani, G. (2012). Estimation of sequencing error rates in short reads. BMC Bioinformatics, 13(1), 1-12.
Article can be found at

Maintained by Victoria Wang (vwang at