Snakefile pipeline of all the steps taken to reconstruct the CIA transcriptome assembly as in (Alfonso-Gonzalez, 2022).

The documentation for this project is hosted at ReadTheDocs.

Occasionally there can be an issue installing R packages in the cia-sqanti environment. This will manifest in an error like this:

Error in if (nzchar(SHLIB_LIBADD)) SHLIB_LIBADD else character() : 
argument is of length zero

if you run into this error, follow the instructions from this thread.