TransPS specifications


Unique identifier OMICS_11469
Name TransPS
Software type Pipeline/Workflow
Interface Command line interface
Restrictions to use None
Input data Input to TransPS includes the set of preassembled contigs and the BLASTX search results containing the alignment of the contigs to the set of reference amino acid sequences.
Output data The output of TransPS includes contigs in three different groups, accepted contigs (A), scaffolded contigs (S), and unused/redundant contigs (R). The contigs in R could be the real redundancy due to genetic variants or different transcripts due to alternative splicing. In order to provide users with detailed account of how the assembly of a particular config is done, a matching map between the original contigs and the corresponding reference protein sequences used in the scaffolding algorithm is also provided.
Operating system Unix/Linux
Programming languages Perl
Computer skills Advanced
Version 1.1.0
Stability Stable
Maintained Yes


No version available


  • person_outline Mingming Liu

Publication for TransPS

TransPS citation


Comparative performance of transcriptome assembly methods for non model organisms

BMC Genomics
PMCID: 4964045
PMID: 27464550
DOI: 10.1186/s12864-016-2923-8

[…] e transcriptome assemblies, contigs were aligned using BLASTX to the Ae. aegypti proteome (AaegL3.3). To provide a second benchmark and minimize potential bias towards reference-based re-assembly and TransPS, the assemblies were also aligned using BLASTX to a non-redundant dipteran protein reference set. This dipteran protein reference set was generated by downloading orthologous protein sequences […]

TransPS institution(s)
Department of Computer Science, Virginia Tech, Blacksburg, VA, USA; Fralin Life Science Institute, Virginia Tech, Blacksburg, VA, USA
TransPS funding source(s)
This work was supported by National Institutes of Health via grant AI085091.

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