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\multirow{2}{*}{Corrector} & \cellc{error after} & \multirow{2}{*}{Mistakes} \\
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ECHO & 40.7 & 17.1 \\
HiTEC & 33.7 & 19.8 \\
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\begin{tabular}{lS[detect-weight,detect-family,table-format=2.2]S[detect-weight,detect-family,table-format=2.2]S[detect-weight,detect-family,table-format=2.2]}
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Corrector & \cellc{N25} & \cellc{N50} & \cellc{N90} \\
& \cellc{kb} & \cellc{kb} & \cellc{kb} \\
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None & 20.7 & 12.1 & 3.54 \\
ECHO & 33.6 & 20.6 & 5.74 \\
HiTEC & 15.6 & 9.76 & 2.75 \\
Coral & 32.2 & 18.0 & 5.48 \\
Quake & 20.3 & 12.7 & 3.38 \\
QuorUM & {\bfseries42.4} & {\bfseries26.3} & {\bfseries7.10} \\
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<ITEXT CH="QuorUM error corrected reads give larger idealized contig sizes for all three measures."/>
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<ITEXT FONT="Liberation Sans Regular" FONTSIZE="40" CH="Guillaume Marçais, Aleksey Zimin, Jim Yorke"/>
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<ITEXT FONTSIZE="30" CH="University of Maryland, College Park, MD 20742-2431"/>
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<ITEXT CH="This project is supported by the following grants: NIH R01HG002945, USDA sub-award 201015739-01, USDA CSREES 2008-04049."/>
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<ITEXT CH="The error corrected reads are aligned against the finished sequence. The number of errors in a read is defined as the length of the read minus the number of unaligned bases (i.e. mismatches and indels). The following plot represents the number of bases (as a percentage of total number of bases in the uncorrected reads) which aligned in reads with 0, 1, 2, 3, 4, or more than 5 errors."/>
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<ITEXT CH="Despite the trimming, QuorUM output the most sequence which aligns to the finished genome. As seen on the following table, almost all of the bases in QuorUM's error corrected reads are in perfect reads (reads with zero errors). "/>
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\begin{tabular}{lr}
\toprule
Corrector & {\# of chimeric reads} \\
\midrule
None & 1555 \\
ECHO & 1764 \\
HiTEC & 3810 \\
Coral & 1253 \\
Quake & 302 \\
Quorum & {\bfseries111} \\
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<ITEXT FONT="Liberation Sans Bold" CH="Abstract."/>
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<ITEXT CH="Illumina Sequencing data can provide high coverage of a genome by relatively short (100-150bp) reads at a low cost. The base error rates in the reads vary greatly along the read sequence. Low quality bases can be trimmed off or error-corrected. Trimming, especially based on the quality scores, can eliminate large amounts of useful sequence in the reads. Error correction is an alternative to trimming that takes advantage of the high coverage of the genome to make the high confidence base corrections in the reads. Error correction allows for more effective use of the sequencing data thus reducing the coverage depth requirements in sequencing projects and increasing the quality of the resulting assemblies. A conservative error correction is also useful for re-sequencing projects: error corrected reads map to the reference much better than the original sequenced reads. The vast majority of errors in Illumina data are substitutions, where a base is read incorrectly. Also, the sequence quality is usually higher on the 5’ end of a read and deteriorates toward the 3’ end of the read. Each base in the read has a quality score associated with it. Based on these observations we developed an error correction technique called QuorUM (Quality Optimized Reads from the University of Maryland, pronounced Quorum). QuorUM corrects substitution errors in Illumina reads with high throughput: 4 billion bases per hour on a 48–core computer. We present the comparisons and timings of QuorUM performance to other available error correction techniques: ECHO, HiTEC, Coral and Quake."/>
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<ITEXT FONT="Liberation Sans Bold" CH="Methods"/>
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<ITEXT CH="The error correctors are compared on the Illumina reads from the PE library of the bacteria "/>
<ITEXT FONT="Liberation Sans Italic" CH="Rhodobacter sphaeroides"/>
<ITEXT FONT="Liberation Sans Regular" CH=" (accession SRX033397). The dataset contains 2 million reads 101bp in length. For the comparison we use the Error Correction Evaluation Toolkit from the Aluru HPC Group (Error correction statistics) and our own metrics (Chimeric reads, Idealized contig sizes and Percentage of initial bases aligned). "/>
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<ITEXT CH="ECHO, HiTEC and Coral only correct reads while Quake and Quorum also trim reads."/>
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\toprule
Corrector & 1 thread & 16 threads & \multicolumn{1}{c}{Speed up\hspace{4mm}} \\
& (minutes) & (minutes) & \\
\midrule
ECHO & 151 & 141 & 1.07 \\
HiTEC & 42 & - & \\
Coral & 87 & 10 & 8.70 \\
Quake & {\bfseries9} & {\bfseries5} & 1.80 \\
QuorUM & 61 & {\bfseries5} & {\bfseries12.2} \\
\bottomrule
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<ITEXT FONT="Liberation Sans Bold" CH="Scalability"/>
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<ITEXT CH="Every error corrector tested, except HiTEC, can work in multi-threaded mode to take advantage of multi-CPU/multi-core machines. For the following table, the timing was performed on a 16-core AMD 2.9Ghz computer with 128GB of RAM running Linux 2.6.35.6."/>
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<ITEXT CH="QuorUM scales well in that setting."/>
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<ITEXT CH="A read is considered chimeric if it two parts (at least 20 bases long) of the read aligns to far apart region of the finished sequence and the read does not align as a whole to the finished sequence."/>
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<ITEXT CH="The error correctors that do not perform trimming (ECHO, HiTEC and Coral) provide only a small improvement or even create new chimeric reads. Only Quake and QuorUM provide a significant improvement."/>
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<ITEXT CH="QuorUM correct and trims Illumina reads with high accuracy and high speed on multi-core machines. The code is available under an open source license at:"/>
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<ITEXT CH="ftp://ftp.genome.umd.edu/pub/quorum/."/>
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<ITEXT FONTSIZE="20" CH="Kao, W.-C., Chan, A. H., & Song, Y. S. (2011). ECHO: A reference-free short-read error correction algorithm. Genome research, 21(7), 1181-1192. doi:10.1101/gr.111351.110"/>
<para PARENT="Citation"/>
<ITEXT CH="Ilie, L., Fazayeli, F., & Ilie, S. (2011). HiTEC: accurate error correction in high-throughput sequencing data. Bioinformatics, 27(3), 295-302."/>
<para PARENT="Citation"/>
<ITEXT CH="Salmela, L., & Schröder, J. (2011). Correcting errors in short reads by multiple alignments. Bioinformatics, 27(11), 1455. Oxford Univ Press."/>
<para PARENT="Citation"/>
<ITEXT CH="Kelley, D. R., Schatz, M. C., & Salzberg, S. L. (2010). Quake: quality-aware detection and correction of sequencing errors. Genome Biol, 11(11), R116. doi:10.1186/gb-2010-11-11-r116"/>
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<ITEXT CH="Yang, X. (2012). A survey of error-correction methods for next-generation sequencing. Briefings in Bioinformatics."/>
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Corrector & {\% bases in perfect reads} \\
\midrule
None & 27.4 \\
ECHO & 68.4 \\
HiTEC & 71.3 \\
Coral & 73.0 \\
Quake & 74.6 \\
QuorUM & {\bfseries98.9} \\
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