global_thaps_clones

Code, scripts, notes, data and supplemental information supporting the paper:

"Sexual ancestors generated an obligate asexual and globally
dispersed clone within the model diatom species _Thalassiosira
pseudonana_," by Julie A. Koester, et al.

Scientific Reports, July 12, 2018. http://www.nature.com/articles/s41598-018-28630-4 DOI: 10.1038/s41598-018-28630-4

All files can be viewed/downloaded via the GitHub web interface. To download (aka "clone") the entire repository, read the following.

Note About Large Files

The "data" subdirectory contains (inter alia) two large files (full.tables.*.rda.gz, about 600 Mb each) summarizing read- and SNP- data for the 7 T. pseudonana isolates. These are stored using Git's "Large File Storage" (LFS) extension https://git-lfs.github.com. If you wish to clone the repo, excluding these files:

1. If you have not installed the LFS extension, just clone as usual -- move to a suitable directory, and issue the command:

   git clone https://github.com/armbrustlab/global_thaps_clones
   

2. If you have installed the LFS extension, do the following (bash syntax) instead of the command listed above:

   GIT_LFS_SKIP_SMUDGE=1 git clone https://github.com/armbrustlab/global_thaps_clones
   

Either will create a subdirectory named "global_thaps_clones", with a total size of about 250 Mb, i.e., a clone of all of the repo except the two large .rda.gz files; short "pointer" files will appear in their place.

If you have installed the LFS extension, step 1 above will clone the full repo, including the large files in "data" (plus a copy of each in git's lfs cache -- for a total repo size of about 2.5 Gb). If you used either approach to exclude the large files, and later decide you want them, either download them via the GitHub web interface, or (after installing LFS) do:

git lfs pull

which will replace both pointer files by the large originals.