vast-tools v2.2.0 released

From VastDB

Published on 12 April 2019, 13:33 by Webadmin
A new version of vast-tools has been released. You can find it in our GitHub repository.

Here is a changelog for the 2.2.0 version:

New features

  • Five new species have been added:

- European amphioxus, `Branchiostoma lanceolatun` (assembly Bl71nemr; species key: `Bla`):

- Centipede, `Strigamia maritima` (assembly Smar1; species key: `Sma`):

- Fruit fly, `Drosophila melanogaster` (assembly BDGP6; species key: `Dme`):

- Worm, `Caenorhabditis elegans` (assembly WBcel235; species key `Cel`):

- Sea anemone, `Nematostella vectensis` (assembly GCA_000209225; species key `Nve`):

Further information about the assemblies and species can be found in the source publication: Torres-Méndez, A., Bonnal, S., Marquez, Y., Roth, J., Iglesias, M., Permanyer, J., Almudí, I., O’Hanlon, D., Guitart, T., Soller, M., Gingras, A.-C., Gebauer, F., Rentzsch, F., Blencowe, B.J.B., Valcárcel, J., Irimia, M. (2019). A novel protein domain in an ancestral splicing factor drove the evolution of neural microexons. Nature Ecol Evol, 3:691-701.

  • `tidy` allows filtering events by coverage using a groups config file. Using this option, the minimum number or fraction of samples with coverage (`--min_N` or `--min_Fr`) applies to EACH group of samples.
  • `combine` allows to create tables of normalized cRPKMs using `normalizebetweenarrays` from the `limma` R package.
  • `compare_expr` provides a list of ranked genes sorted by fold change to be used directly in GSEA (with rnk.txt extension).
  • `compare` provides the list of all AS events with coverage, when the option `--GO` is provided.

Updates and fixes

  • Quality control to make sure the expression files have the same number of genes when combining.
  • Improvements in README and help messages.
  • Various other minor fixes and improvements.