v2.2.0

NEW

• Five new species have been added:

  • European amphioxus, Branchiostoma lanceolatun (assembly Bl71nemr; species key: Bla): http://vastdb.crg.eu/libs/vastdb.bla.01.12.18.tar.gz

  • Centipede, Strigamia maritima (assembly Smar1; species key: Sma): http://vastdb.crg.eu/libs/vastdb.sma.01.12.18.tar.gz

  • Fruit fly, Drosophila melanogaster (assembly BDGP6; species key: Dme): http://vastdb.crg.eu/libs/vastdb.dme.01.12.18.tar.gz

  • Worm, Caenorhabditis elegans (assembly WBcel235; species key Cel): http://vastdb.crg.eu/libs/vastdb.cel.01.12.18.tar.gz

  • Sea anemone, Nematostella vectensis (assembly GCA_000209225; species key Nve): http://vastdb.crg.eu/libs/vastdb.nve.01.12.18.tar.gz

    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.

• Added official Docker container image at: https://cloud.docker.com/u/vastgroup/repository/docker/vastgroup/vast-tools.

• Included continuous integration tests with TravisCi: https://travis-ci.org/vastgroup/vast-tools.

• 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

• The VASTDB libraries for zebrafish (Dre) and sea urchin (Spu) have been updated (http://vastdb.crg.eu/libs/ vastdb.dre.01.12.18.tar.gz and http://vastdb.crg.eu/libs/vastdb.spu.01.12.18.tar.gz). A few new microexons are now included in the MIC module.
• 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.