Super deduper, fast PCR duplicate detection in fastq files.

BCB 2015 - 6th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics

Volumn , Issue , 2015, Pages 491-492

  Petersen, Kristen R ^a   Streett, David A ^a   Gerritsen, Alida T ^a   Hunter, Samuel S ^a   Settles, Matthew L ^a  

^a UNIVERSITY OF IDAHO   (United States)

Author keywords

High throughput sequencing; PCR duplicates; Short read alignment

Indexed keywords

BIOINFORMATICS; INFORMATION SCIENCE;

ALIGNMENT TECHNIQUE; DUPLICATE DETECTION; FAST PCR; HIGH-THROUGHPUT SEQUENCING; OPEN SOURCE APPLICATION; PCR DUPLICATES; PRE-ALIGNMENT; SHORT-READ ALIGNMENTS;

ALIGNMENT;

EID: 84963627112     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1145/2808719.2811568     Document Type: Conference Paper

References (9)

1. Burriesci, M. S., Lehnert, E. M., Pringle, J. R. 2012. Fulcrum: condensing redundant reads from high-throughput sequencing studies. Bioinformatics (Oxford, England), 28(10), 1324-7.
2. Faust, G. G., Hall, I. M. 2014. SAMBLASTER: fast duplicate marking and structural variant read extraction Bioinformatics, 30(17): 2503-2505.
3. Langmead, B., & Salzberg, S. 2012. Fast gapped-read alignment with Bowtie 2. Nature Methods, 357-359
4. Li, H., Durbin, R. 2009. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics, 25, 1754-1760.
5. Pireddu, L., Leo, S., Zanetti, G. 2011. SEAL: a distributed short read mapping and duplicate removal tool. Bioinformatics, 27(15), 2159-2160.
6. Ruopp, M. D., Perkins, N. J., Whitcomb, B. W., & Schisterman, E. F. 2008. Youden Index and optimal cut-point estimated from observations affected by a lower limit of detection. Biometrical Journal. Biometrische Zeitschrift, 50(3), 419-30.
7. Shinzato C., Shoguchi E., Kawashima T., Hamada M., Hisata K., et al. 2011. Using the Acropora digitifera genome to understand coral responses to environmental change. Nature 476: 320-323.
8. Tarasov, A., Vilella, A. J., Cuppen, E., Nijman, I. J., Prins, P. 2015. Sambamba: fast processing of NGS alignment formats. Bioinformatics
9. Xu, H., Luo, X., Qian, J., Pang, X., Song, J., et al. 2012. FastUniq: a fast de novo duplicates removal tool for paired short reads. PloS One, 7(12), e52249.