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PanOCT: Automated Clustering of Orthologs using Conserved Gene Neighborhood for Pan-Genomic Analysis of Bacterial Strains and Closely Related Species. Derrick E. Fouts, Lauren Brinkac, Erin Beck, Jason Inman, and Granger Sutton. Nucleic Acids Res 2012 40(2):e172.
**NEW Publication in Genome Biology featuring PanOCT for pan-chromosome consensus building was featured in "This Week in Genome Biology":
A novel method of consensus pan-chromosome assembly and large-scale comparative analysis reveal the highly flexible pan-genome of Acinetobacter baumannii. Agnes P. Chan, Granger Sutton, Jessica DePew, Radha Krishnakumar, Yongwook Choi, Xiao-Zhe Huang, Erin Beck, Derek M. Harkins, Maria Kim, Emil P. Lesho, Mikeljon P. Nikolich and Derrick E. Fouts. Genome Biol 2015 16(143):1-28.
See Dr. Sutton's talk on PanOCT at The 13th Genomic Standards Consortium Meeting (GSC 13). Hosted by BGI and held at Kingkey Palace Hotel, Shenzhen, China, March 4-7, 2012: http://www.scivee.tv/node/46402
Memory usage guide (based on 4 Mbp bacterial genomes)
| Memory | # genomes |
|---|---|
| 1 GB RAM | 1-5 |
| 2 GB RAM | 1-8 |
| 4 GB RAM | 1-12 |
| 8 GB RAM | 1-18 |
| 14 GB RAM | 1-25 |
*Note: This is only meant as a guide. Performance may very. Results not guaranteed.
**Please see the Wiki to download the supplemental files from the paper.