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A fast solution for improving long reads accuracy by short read alignment

Introduction

The single molecule, real time (SMRT) sequencing technology of Pacific Biosciences made it possible to acquire transcripts from end to end with its extraordinary long reads (> 10kb). This new method of transcriptome study has been applied on several remarkable projects on human or other model organisms. However, the raw data of SMRT sequencing present a relative low quality with random error rate at about 15%, which the error correction using the next generation sequencing (NGS) short reads was necessary in general. Here we report an improved tools named LSCplus, using the LSC program as a reference. LSCplus greatly reduced the running time, and provide high accuracy.

Getting Started

• Check Requirements for running LSCplus.
• Read the Example data.
• Prepare Datasets for LSCplus.
• Prepare Configuration file for LSCplus.
• Download the latest version of LSCplus.
• Follow the Tutorial to run LSCplus.
• Get the results.

Please refer the Wiki Documentation Page for More details

Note

• LSCplus_cpp: Error Correction Step is implemented in C++;
• LSCplus_Pyhon: Error Correction Step is implemented in Python.