A Review of Pangenome Tools and Recent Studies
- PMID: 32633917
- Bookshelf ID: NBK558826
- DOI: 10.1007/978-3-030-38281-0_4
A Review of Pangenome Tools and Recent Studies
Excerpt
With the advance of sequencing technologies, the landscape of genomic analysis has been transformed, by moving from single strain to species (or even higher taxa)-wide genomic resolution, toward the direction of capturing the “totality” of life diversity; from this scientific advance and curiosity, the concept of “pangenome” was born. Herein we will review, from practical and technical implementation, existing projects of pangenome analysis, with the aim of providing the reader with a snapshot of useful tools should they need to embark on such a pangenomic journey.
Copyright 2020, The Author(s).
Sections
- 1. Introduction
- 2. Technical Implementation
- 3. Bayesian Decision Model
- 4. BGDMdocker
- 5. Bacterial PanGenome Analysis
- 6. ClustAGE
- 7. DeNoGAP
- 8. EDGAR
- 9. EUPAN
- 10. GET_HOMOLOGUES
- 11. Harvest
- 12. ITEP
- 13. LS-BSR
- 14. micropan
- 15. NGSPanPipe
- 16. PanACEA
- 17. Panaconda
- 18. PanCake
- 19. PanFunPro
- 20. PanGeT
- 21. PanGFR-HM
- 22. PanGP
- 23. PANINI
- 24. PANNOTATOR
- 25. PanOCT
- 26. Panseq
- 27. Pan-Tetris
- 28. PanTools
- 29. PanViz
- 30. PanWeb
- 31. panX
- 32. PGAdb-Builder
- 33. PGAP
- 34. PGAP-X
- 35. Piggy
- 36. pyseer
- 37. Roary
- 38. seq-seq-pan
- 39. Spine and AGEnt
- 40. SplitMEM
- 41. Highlights
- 42. Food for Thought
- 43. Conclusions
- References
References
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- Abudahab K, Prada JM, Yang Z, Bentley SD, Croucher NJ, Corander J, Aanensen DM (2018) PANINI: pangenome neighbour identification for bacterial populations. Microb Genom 5(4). https://doi.org/10.1099/mgen.0.000220 - DOI - PMC - PubMed
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- Ahmed A, Earl J, Retchless A, Hillier SL, Rabe LK, Cherpes TL, Powell E, Janto B, Eutsey R, Hiller NL et al (2012) Comparative genomic analyses of 17 clinical isolates of Gardnerella vaginalis provide evidence of multiple genetically isolated clades consistent with subspeciation into genovars. J Bacteriol 194(15):3922–3937 - PMC - PubMed
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