ABOUT

TransPS is a pipeline for post-processing of pre-assembled transcriptomes using reference based method. It applies an align-layout-consensus structure, consisting of three major stages. First, query sequences are aligned with a reference genome. Second, query sequences are ordered based on the alignment to the reference. Third, non-redundant sequences matched to the same gene of reference genome are scaffolded into one contig.

The results show that the post processed transcriptome removed the redundant contigs while having significant higher coverage ratio than the original transcriptome.

USAGE

Prerequisites

NCBI Blast -- Please download and install the NCBI Blast+ 2.2.26 or later version form here by following the instructions.

A reference species -- Protein sequences of a closely related organism.

Perl 5 -- The programming was written in perl. Please have perl 5.12.4 or later version installed.

String::LCSS_XS -- A perl module for finding The longest common substring of two strings. You can find it here.

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CITATION

If you are going to use TransPS, please cite the following paper:

A Transcriptome Post-Scaffolding Method for Assembling High Quality Contigs," Computational Biology Journal, vol. 2014, Article ID 961823, 4 pages, 2014. doi:10.1155/2014/961823

CONTACTS

This work was supported by National Institutes of Health via grant AI085091. The author thanks Dr. Adelman and Dr. Zhang for helpful discussion and comments. We appreciate any feedbacks! Please send comments and suggestions to Mingming Liu at mingml@vt.edu.

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