Software

Software I've developed (primary or co-developer)

  1. Bambus 2: a scaffolder for metagenomic data
    • Repository: https://sourceforge.net/projects/amos/files/amos/3.1.0/
    • Status: Maintenance mode
    • Publication: Koren S, Treangen TJ, Pop M. Bambus2: Scaffolding Polymorphic Genomes and Metagenomes. Bioinformatics. 2011 Sep 16. PMID: 21926123.
  2. Mash: Fast similarity estimates via MinHash
    • Repository: github.com/marbl/mash
    • Status: Active development (primary developer Brian Ondov)
    • Publication: Ondov BD, Treangen TJ, Koren S, Phillippy AM. Mash: fast genome and metagenome distance estimation using MinHash, Genome Biology, 2015.
  3. MetaForge : use-case and validation centric metagenomics
    • Repository: TBA
    • Status: Active development
    • Publication: In prep
  4. MetaCarvel (aka Bambus 3):
    • Repository: https://github.com/marbl/bambus3
    • Status: Active development (primary developer Jay Ghurye)
    • Publication: In prep
  5. MetaCompass
    • Repository: https://github.com/marbl/metacompass
    • Status: Active development
    • Publication: Under review
  6. MetAMOS: a metagenomic NGS assembly pipeline
    • Repository: https://github.com/marbl/metamos
    • Status: Maintenance mode
    • Publication: Treangen, TJ., et al. "MetAMOS: a modular and open source metagenomic assembly and analysis pipeline." Genome biology 14.1 (2013): R2.
  7. MetaPhyler: metagenomic profiling
    • Repository: https://github.com/marbl/metaphyler
    • Status: Maintenance mode
    • Publication: Liu B, Gibbons T, Ghodsi M, Treangen TJ, Pop M. Accurate and Fast Estimation of Taxonomic Profiles from Metagenomic Shotgun Sequences. BMC Genomics. 2011;12:S2 .
  8. Parsnp: rapid, interactive SNP typing for microbial genomes.
    • Repository: https://github.com/marbl/parsnp
    • Status: Maintenance mode
    • Publication: Treangen TJ, Ondov B, Phillippy AM. Rapid Core-Genome Alignment and Visualization for Thousands of Intraspecific Microbial Genomes. Genome Biology. 2014
  9. Repeatoire:
    • Repository: https://sourceforge.net/p/mauve/code/HEAD/tree/repeatoire/
    • Status: Maintenance mode
    • Publication: Treangen, T. J., Darling, A. E., Achaz, G., Ragan, M. A., Messeguer, X., & Rocha, E. P. (2009). A novel heuristic for local multiple alignment of interspersed DNA repeats. IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), 6(2), 180-189.
  10. VALET
    • Repository: https://github.com/marbl/valet
    • Status: Active development
    • Publication: Under review

Software organizations

Other Contributions

  • AMOS
    • I helped develop version 3 with improvements to the bank related to Bambus 2 development efforts
  • Mauve
    • I helped to integrate libMUSCLE and contributed code for HMM-based LCB extension