These are the essential scripts developed in the assembly of the red fox genome. They are made available here in case they can be useful for future analyses.
essential_mods.py is a set of very simple functions that we used to pull sequence from the scaffolds and orient it appropriately.
racaout_to_csv.py takes RACA's output files and transforms them to a csv format that is easier to use for analysis (in Excel, Python, R, etc.)
make-frags.py takes the scaffolds and the RACA input to make the fasta files that comprise 1) RACA's assembly, and 2) the chromosome fragment assembly. It depends on:
- A comma-separated file (here: racafrag_foxfrag.csv) that specifies the relationship between RACA fragments and fox fragments. It shoudl have a header (Fragment,FoxSeg) and each line should list the RACA Fragment and its associated Chromosomal Fragment (e.g. 26a,10
- Syntenic relationships between the dog (reference) and fox (target) species, which are hard-coded into the script here as a list (line 113)
- the essential_mods.py functions
- RACA's output
- The scaffolds
You can reach out to me at rando2 at Illinois dot edu if you have any questions.
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Copyright (c) [2018] [Halie M. Rando]
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