Quality check and analysis of Illumina NGS data

[subuhikhan]

Hello,

I am working with RNAseq Illumina data. I have already checked the quality of all seq libraries by FastQC. At present I have used Geneious to create assembly of each of my library against reference seq. But Geneious is not a specialized software that can handle Illumina NGS data. Are there any software's that I can for carrying out analysis of my data? And is there any program that can allow identification and trimming of poor quality sequences?

Thank you
Subuhi

[GW_OK]

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