Editing BioMicroCenter:Research (section)

=== Processing Very Long Illumina Reads - [http://web.mit.edu/biology/www/facultyareas/facresearch/chisholm.html CHISHOLM LAB] - [http://web.mit.edu/biology Biology] ===
Different high-throughput sequencing platforms are currently available, and trade-offs currently exist between the cost per sequencing read, the number of reads, and the average read length. The Chisholm lab has been interested in optimizing the Illumina platform for the de novo sequencing of microorganisms. To this end, the Chisholm lab has worked with the BioMicro Center to develop a pipeline that significantly increases the read length yielded by the Illumina sequencing technology, generating sequencing reads that can exceed 250 nucleotides in length. Combined with Illumina's low cost and high-throughput, the procedure expands the range of applications that can be performed with this platform. <BR><BR>
Illumina reads tend to decrease in quality with length due to slight errors in incorporation and extension of the growing sequence. To improve the error rate at long read lengths, the Chisholm lab developed an algorithm SHERA (SHortread Error-Reducing Aligner) which uses overlapping paired-end reads to  create long and accurate composite reads. SHERA allows more than 87% of the paired-end sequencing reads to produce longer composite sequences with less than 1% of paired reads incorrectly aligned. The quality score of each overlapped base is re-evaluated to take into account the information from the two paired-end reads. The Chisholm lab sequenced a marine metagenomic DNA sample using 454-FLX and the Illumina paired-end overlapping procedure, and found that the taxonomic classification results are highly platform-independent, demonstrating that that composite sequencing reads constitute a cost-effective alternative to pyrosequencing. <BR><BR>
The creation of high-quality very long Illumina reads is not only applicable to metagenomics sequencing. The BioMicro Center is currently working to deploy this algorithm for many other applications including amplicon sequencing, transcriptomics, de novo assembly and resequencing for mutation detection. We anticipate a strong growth in very long reads in FY2011. This work has been accepted for publication in PLoS One.