TransPS statistics

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TransPS specifications

Information


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

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Maintainer


  • person_outline Mingming Liu <>

Publication for TransPS

TransPS in publication

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

[…] including a widely used de novo assembler (trinity), two transcriptome re-assembly strategies utilizing proteomic and genomic resources from closely related species (reference-based re-assembly and transps) and a genome-guided assembler (cufflinks)., these four assembly strategies were compared using a comprehensive transcriptomic database of aedes albopictus, for which a genome sequence […]


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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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