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Trans-ABySS | De novo assembly and analysis of RNA-seq data

Allows users to analyze ABySS-assembled contigs from shotgun transcriptome data. Trans-ABySS is a standalone software composed of two modules: transabyss that performs assembling of RNAseq data and transabyss-merge that allows to merge assemblies derived from the first feature. The application includes a gene-level expression metric based on reads aligned to contigs that can be used with or without an annotated reference genome.

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Trans-ABySS classification

Trans-ABySS specifications

Unique identifier:
OMICS_01326
Interface:
Command line interface
Operating system:
Unix/Linux
Computer skills:
Advanced
Stability:
Stable
Maintained:
Yes
Software type:
Application/Script, Package/Module
Restrictions to use:
Academic or non-commercial use
Programming languages:
Python
Version:
1.5.5
Requirements:
ABySS, python-igraph, BLAT

Trans-ABySS distribution

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Trans-ABySS support

Documentation

Maintainers

  • Inanc Birol <>
  • Readman Chiu <>

Additional information

https://github.com/bcgsc/transabyss

Credits

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Publications

Institution(s)

Canada’s Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada; Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, BC, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada

Funding source(s)

Supported, in part, by Genome Canada, Genome British Columbia, Michael Smith Foundation for Health Research and the Canadian Institute of Health Research (CIHR), including the CIHR Bioinformatics Training Program for Health Research.

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