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STM | Optimization of de novo transcriptome assembly from next-generation sequencing data

Allows de-novo assembly of transcriptome using a reference proteome. STM exploits the fact that, by translating contigs into amino acid sequences, it is possible to search for orthologous regions in a reference proteome, even when it belongs to a distantly related organism. The method can join multiple transcript fragments that are part of a single gene, providing new and valuable information on the order and the orientation of these fragments along original transcript. Multiple- k, a method that performs multiple assemblies with various k-mer lengths and retains the best part of each one to form the final assembly is also available.

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STM forum

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STM classification

STM specifications

Unique identifier:
OMICS_01325
Software type:
Application/Script
Restrictions to use:
None
Computer skills:
Advanced
Source code URL:
http://www.surget-groba.ch/downloads/stm.tar.gz
Name:
Scaffolding using Translation Mapping
Interface:
Command line interface
Operating system:
Unix/Linux
Stability:
Stable
Maintained:
Yes

Subtools

  • Multiple-k

STM distribution

versioning

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No versioning.

STM support

Maintainer

  • Juan Montoya-Burgos <>

Credits

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Publications

Institution(s)

Department of Zoology and Animal Biology, University of Geneva,Geneva, Switzerland

Funding source(s)

Supported by funds from the Canton de Geneve, the Swiss National Research Fund (Number 3100A0-
122303/1), and the G & A Claraz Foundation.

By using OMICtools you acknowledge that you have read and accepted the terms of the end user license agreement.