project
|- README          # the top level description of content
|
|- doc/            # documentation for the study
|  |- notebook/    # preliminary analyses (dead branches of analysis)
|  +- paper/       # manuscript(s), whether generated or not
|
|- data            # raw and primary data, are not changed once created
|  |- references/  # reference files to be used in analysis
|  |- raw_june/    # raw data from june sequencing
|  |- raw_october/ # raw data from october sequencing
|  |- mothur_june/ # processing of june data with mothur
|  |- mothur_october # processing of october data with mothur
|  +- process/     # cleaned data, will not be altered once created;
|                  # will be committed to repo
|
|- code/           # any programmatic code
|  |
|  +- smrtanalysis/smrtcmds/bin/ #PacBio software. exe's are here
|
|- results         # all output from workflows and analyses
|  |- tables/      # text version of tables to be rendered with kable in R
|  |- figures/     # graphs, likely designated for manuscript figures
|  +- pictures/    # diagrams, images, and other non-graph graphics
|
|- scratch/        # temporary files that can be safely deleted or lost
|
|- Schloss_PacBio16S_PeerJ_2016.Rmd	# Rmarkdown for this study
|
|- submission		# stuff to be submitted
|	|- Schloss_PacBio16S_PeerJ_2016.md		# Markdown version of the *Rmd file
|	|- Schloss_PacBio16S_PeerJ_2016.pdf		# pdf version of the *Rmd file
|	|- various figures and tables
|	+- rebuttal_v1.pdf						# response to reviewers' comments
|
+- Makefile        # executable Makefile for this study, if applicable