DOIAbstract
Summary cDNA libraries from fruit fly, leopard, rat and canary were downloaded from Ensembl [1]. For each ≈10 million read pairs, of length 200 nt, insert size 300 nt and containing no read error, were generated from transcripts that ranged in length from 300 to 5000 nt in a manner that reflects uniform coverage. Further details are described in our manuscript: "CStone: A de novo transcriptome assembler for short-read data that identifies non-chimeric contigs based on underlying graph structure" [2]. Use of such simulated data allows for the comparison of the assembled contigs to the sequences from which the reads were derived, while excluding the effects of unknown variation; including that of sequencing error and poor coverage. The CSton...
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