Computational analysis of potato (Solanum tuberosum) transcriptomic RNA-seq data quality using CLC workbench

Abstract

The CLC de novo assembler is a support system for large data sets and integrated scaffolding for joining contigs based on paired reads information. It is designed to accept a combination of data from Illumina, 454, SOLiD, Ion Torrent and Sanger sequencing as a mix of paired and unpaired reads which allows the quality analysis of SRA data from different sequencing technologies, to be exploited. In the present study, transcriptome data of three different physiological stages of potato tubers i.e. Dormant tuber (DT), Dormancy release tuber (DRT) and Sprouting tuber (ST) were studied for computational quality analysis. A total no. of 38,714,870 paired sequences of DT (ID: SRR1039535), 38,669,102 paired sequences of DRT (ID: SRR1103933) and 38,753,150 paired sequences of ST (ID: SRR1103934) were downloaded from SRA database in FastQ format. The De novo assembly resulted with 50849 (DT), 44550 (DRT) and 46254 (ST) contigs. The values for N50 and average contig length recorded 1,016(DT), 1,118 (DRT), 1,015 (ST) and 680(DT), 725(DRT), 685(ST) respectively They have been analysed for quality check with the Per-sequence analysis, Per-base and Over-representation analysis using CLC workbench which includes different categories resulting in good quality of data.