Eurycea Genomics Project
Find a phylogenetics-focused workshop using these data here
Find a data matrix assembly-focused workshop here
Files for eurycea project. Descriptions follow:
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JA14300popmap, JA14785popmap and total_popmap: Barcodes sorted by individual, for each sequencing run separately, and both combined. For more information on why these barcode files are need it, please see this paper on ddRAD sequencing.
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Converter.py: short script using the dendropy 3.x library to convert between file formats. Usage:
python converter.py 'path to files' 'extension of files' 'format of input files' 'format you'd like exported'Example
+ Populations, cstacks, sstacks, ustacks, process_rad: Scripts for the [Stacks](http://catchenlab.life.illinois.edu/stacks/)
pipeline
+ relabel_str.py: Relabeling script, as Stacks outputs files with their numerical names,
rather than their locality data. Would be smart to change this to take an input file of
names, rather than having them hardcoded, but I never got around to it.
+ Rename.py: modification of script from Becca Tarvin to rename files output from process_rad,
which are named for their barcodes. Could combine this and relabelstr.py to add in the
locality data earlier.
+ Renexus.py: This is actually the same script as relabelstr.py. I should delete one of
them, but it feels ... dishonest?