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J Biomol Tech. 2010 September; 21(3 Suppl): S20.
PMCID: PMC2918134

Transcriptome Assembly of Next-Generation Sequencing Data Using NextGENe Software and the Condensation Tool

M. Manion, H. Ren, J. Wu, S. Ni, and C.S.J. Liu
SoftGenetics, State College, PA, United States



The assembly of transcriptomes is a difficult challenge due to the complexity of transcriptomes which include multiple isoforms of various transcripts resulting in many highly similar sequences.When high throughput sequence reads are used, the short read lengths often are not long enough to cover an entire exon or exons with retained introns.NextGENe's novel Condensation Tool is used to cluster reads containing similar sequences to statistically correct sequencing errors.The first cycle uses 12mer anchor sequences and 12bp flanking sequences to sort reads into groups and subgroups to generate a consensus.The second cycle and any additional cycles incrementally elongate reads by merging similar contigs, allowing minimum variation.In this way, NextGENe Software's Condensation Tool overcomes many of the challenges involved with the analysis of next generation sequencing data.By clustering similar reads, data is polished, removing low frequency, biased sequencing errors while maintaining true variations.Reads are lengthened to provide a more unique sequence greatly increasing assembly accuracy. Following Condensation, overlapping paired end reads can be linked to generate single reads spanning the entire library, up to 1000bp.

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