Software
- 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.
- 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.
- MetaForge : use-case and validation centric metagenomics
- Repository: TBA
- Status: Active development
- Publication: In prep
- MetaCarvel (aka Bambus 3):
- Repository: https://github.com/marbl/bambus3
- Status: Active development (primary developer Jay Ghurye)
- Publication: In prep
- MetaCompass
- Repository: https://github.com/marbl/metacompass
- Status: Active development
- Publication: Under review
- 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.
- 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 .
- 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
- Repeatoire:
- Repository: TBD (old --> https://sourceforge.net/p/mauve/code/HEAD/tree/repeatoire)
- Status: Active Development
- Developer: Advait Balaji
- 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.
- S2FAST:
- Repository: TBD
- Status: Active Development
- Developer: Dan Nasko
- Publication: In prep.
- VALET
- Repository: https://github.com/marbl/valet
- Status: Active development
- Publication: Under review
Software organizations
Software organizations