A Comparison of 454 and Illumina for RNA-sequencing

Rob Gentleman
Fred Hutchinson Cancer Research Center

We recently carried out deep sequencing of two cell lines using both 454 and Illumina sequencing. The former were single long sequences (about 430nt each) while the latter were 75nt paired end sequences. The sequences were aligned to the genome using gMAP (Wu and Watanabe, 2005) and gSNAP (Wu and Nacu, 2010), http://research-pub.gene.com/gmap.
We then performed a detailed comparison of the two methodologies and in the presentation I will contrast their strengths and weaknesses. Particular attention will be paid to features where one of the two technologies appears to give a substantial advantage.
1) Thomas D. Wu and Colin K. Watanabe
GMAP: a genomic mapping and alignment program for mRNA and EST sequences
Bioinformatics 2005 21: 1859-1875 2) Thomas D. Wu and Serban Nacu
Fast and SNP-tolerant detection of complex variants and splicing in short reads
Bioinformatics 2010 26: 873-881

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