TriMetAss – The Trinity-based Iterative Metagenomics Assembler
Johan Bengtsson-Palme, 2013

TriMetAss is an extension to the Trinity software [1], which can assemble select regions surrounding interesting features in metagenomic data. The software is particularly useful for very common and well-conserved genes (and – in theory – non-coding regions) that can occur in multiple contexts in the microbial community under study. It uses Vmatch [2] to extend seed reads (or contigs generated by another assembler) into longer contigs, by iteratively calling Vmatch and Trinity, until some stop criteria are met. Currently, TriMetAss lacks a thorough documentation, but you can direct questions to me if the README.txt file and the “-h” option is not sufficient to understand the software. To use TriMetAss, you need to download and install the Vmatch and Trinity software packages from the links found below.

Download TriMetAss (version 1.2)

Download Trinity
Download Vmatch

If you use TriMetAss in your research, please cite the following paper in which it is briefly described:

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

Please report bugs to my: first name (dot) last name (at) microbiology (dot) se

Version history

  • 4th February 2016 – 1.6 – Improved support for newer Trinity versions, bug fixes.
  • 1st July 2015 – 1.1 – Better stopping control, support for multiple input files, support for newer Trinity versions, bug fixes.
  • 9th December 2013 – 1.0 – first public release.

Contact information

Johan Bengtsson-Palme (firstname.lastname [at] microbiology.se)
University of Gothenburg
Department of Infectious Diseases, Institute of Biomedicine

References

  1. Grabherr, M. G. et al. Full-length transcriptome assembly from RNA-Seq data without a reference genome. Nat Biotechnol 29, 644–652 (2011).
  2. Kurtz, S. The Vmatch large scale sequence analysis software (2010). http://vmatch.de/