TransPS specifications

Unique identifier:
OMICS_11469
Interface:
Command line interface
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.
Operating system:
Unix/Linux
Computer skills:
Advanced
Stability:
Stable
Software type:
Pipeline/Workflow
Restrictions to use:
None
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.
Programming languages:
Perl
Version:
1.1.0
Maintained:
Yes

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TransPS support

Maintainer

  • Mingming Liu <>

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Publications

Institution(s)

Department of Computer Science, Virginia Tech, Blacksburg, VA, USA; Fralin Life Science Institute, Virginia Tech, Blacksburg, VA, USA

Funding source(s)

This work was supported by National Institutes of Health via grant AI085091.

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