The comparison of assembler using transcriptome data from Dracocephalum kotschyi Boiss

with fast advances in next generation sequencing technologies, they has become powerful and low-cost tools for transcriptome studies, Nowadays; de novo assembly of transcriptome data, has caused the formation of the new pathway in the study of non-model genome species [1]. With the expansion of this technology and increasing the number of assembly softwares, choosing the best software for assembling transcriptome sequencing data has become a challenge for biologists. Dracocephalum kotschyi is one of the medicinal plants belong to labiatae family and native to Iran. In traditional medicine, this plant is used for treatment fever, joint pain, rheumatism as well an anti-inflammatory [2,3]. It contains wide range of terpenoides and flavonoids [3]. For the first time in this study, total RNA form D. kotschyi were sequenced on illumina platform as paired end sequencing with 40M reads and 150bp of length, then the transcriptome sequencing data were applied in order to reach the appropriate parameters and superior software. After quality control and trimming raw reads, we used Oases-velvet [4], SOAPdenovo-Trans [5], Trans-ABySS [6] and Trinity [7] softwares with two different values of K parameter (K=25 and K=32) for assembling qualiffied reads. Then, we used Bowtie2 [8] to map reads to assembled contigs for getting alignment rate and number of mapped reads. Eventually, the results generated a total of thirty different files and all of the assemblies were compared to each others in the term of several criteria including: N50, sequence number, average, minimum and maximum length of reconstructed sequences, alignment rate, number of mapped reads and runtime. The final result suggests the superiority of Trinity and Trans-ABySS softwares.

کلیدواژه ها:

Trinity ، Illumina ، SOAPdenovo-Trans ، Oases-velvet ، Trans-ABySS