vast-tools v1.3.0 has been released

From VastDB

Published on 24 November 2017, 13:04 by Transdevo
Christmas has come early for the vast-tools team! We are happy to announce that the new version of vast-tools (v1.3.0) has been released. The main improvements in this new version are:
  • Two new species: zebrafish (Danio rerio, assembly danRer10), and sea urchin (Strongylocentrotus purpuratus, assembly Spur 3.1).
  • New coverage scoring criteria for alternative 3'/5' splice site events. Scoring for these events is now more strict.
  • A --resume option in the align command, which can be used when re-running align runs that have been interrupted.
  • A new tidy module, to turn vast-tools raw output tables into matrices ready to upload into R, after applying simple filtering criteria.
  • An improved plot module, which can now plot gene expression (in cRPKM) using --expr=TRUE
  • The main citation for vast-tools is now:

Tapial, J., Ha, K.C.H., Sterne-Weiler, T., Gohr, A., Braunschweig, U., Hermoso-Pulido, A., Quesnel-Vallières, M., Permanyer, J., Sodaei, R., Marquez, Y., Cozzuto, L., Wang, X., Gómez-Velázquez, M., Rayón, M., Manzanares, M., Ponomarenko, J., Blencowe, B.J., Irimia, M. (2017). An Alternative Splicing Atlas Reveals New Regulatory Programs and Genes Simultaneously Expressing Multiple Major Isoforms in Vertebrates. Genome Res, 27(10):1759-1768

  • The citation for the zebrafish and sea urchin databases is:

Burguera, D., Marquez, Y., Racioppi, C., Permanyer, J., Torres-Mendez, T., Esposito, R., Albuixech, B., Fanlo, L., D'Agostino, Y., Gohr, A., Navas-Perez, E., Riesgo, A., Cuomo, C., Benvenuto, G., Christiaen, L.A., Martí, E., D'Aniello, S., Spagnuolo, A., Ristoratore, F., Arnone, M.I., Garcia-Fernàndez, J., Irimia, M. (2017). Evolutionary recruitment of flexible Esrp-dependent splicing programs into diverse embryonic morphogenetic processes. Nat Commun, In press.

The full changelog, and the code can be found at our GitHub repository, here.

Happy analyses!