ESTclean – A Cleaning Tool for RNA-Seq

ESTclean is a program designed to clean raw sequences with seven modules that perform end sequence trimming, barcode trimming, sequencing adapter trimming, amplification primer trimming, poly-A tail trimming, vector screening and low quality region trimming. These modules can be combined based on various sequencing applications, e.g., parallel tagged sequencing. ESTclean provides a GUI with a user-friendly environment to manage sequencing protocols and analysis pipelines. It also produces various summary tables and figures to aid quality control by showing trimming statistics for each module; identifying problematic reads with primer concatenation, wrongly oriented primers, and no barcodes; and assessing sequencing biases.

Availability –


  •  Tae H, Ryu D, Sureshchandra S, Choi JH. (2012) ESTclean: A Cleaning Tool for Next-Gen Transcriptome Shotgun Sequencing. BMC Bioinformatics 13(1), 247. [Epub ahead of print]. [abstract]