Trinity 2.13.2 – RNA-Seq De novo Assembly

Trinity 2.13.2

:: DESCRIPTION

Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes.

::DEVELOPER

The Broad Institute, Cambridge, MA

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX
  • Java

:: DOWNLOAD

Trinity

:: MORE INFORMATION

Citation

Manfred G. Grabherr, Brian J. Haas, […], and Aviv Regev
Trinity: reconstructing a full-length transcriptome without a genome from RNA-Seq data
Nat Biotechnol. 2011 May 15; 29(7): 644–652. doi: 10.1038/nbt.1883

TriMetAss 1.2 – The Trinity-based Iterative Metagenomics Assembler

TriMetAss 1.2

:: DESCRIPTION

TriMetAss is an extension to the Trinity software , which can assemble select regions surrounding interesting features in metagenomic data

::DEVELOPER

The Bengtsson-Palme Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux  / MacOsX
  • Java
  • Trinity

:: DOWNLOAD

 TriMetAss

:: MORE INFORMATION

Citation:

Bengtsson-Palme J, Boulund F, Fick J, Kristiansson E, Larsson DGJ:
Shotgun metagenomics reveals a wide array of antibiotic resistance genes and mobile elements in a polluted lake in India.
Frontiers in Microbiology, Volume 5, Issue 648 (2014). doi: 10.3389/fmicb.2014.00648