Ground-truthing Phylotype Assignments for Antarctic Invertebrates

Introduction

The following code represents analyses conducted for the manuscript titled Ground-truthing Phylotype Assignments for Antarctic Invertebrates, DNA Barcodes 2017, 4: 26–38, DOI 10.1515/dna-2017-0001. Use git clone or your favourite Git manager to download these files to your system. Please do not execute the scripts on your system without looking at them first. Please contact me should you have questions, I will attempt to help you if time permits.

Disclaimer

THIS SOFTWARE IS PROVIDED "AS IS" AND ANY EXPRESSED OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE REGENTS OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

System requirements

1. R environment (currently using R 3.2.0 - R packages employed for analysis, are listed in file ./160621_package_citations.bib. This file can be opened with most common reference managers)
2. Bash shell (OSX 10.10.5) - Should you work in a different environment consider adopting the line endings of files as well as syntax differences in tools such as sed or grep.
3. MacQiime (Qiime 1.8., later versions of Qiime may have slight syntax differences).

Contents

Directories

• 0_AU_SOIL_biom_files_18S/: .biom files for 18S data from Australian soils generated with variable thresholds as described in the manuscript.
• 0_AU_SOIL_biom_files_COI/: .biom files for COI data from Australian soils generated with variable thresholds as described in the manuscript.
• 1_AU_MOCK_biom_files_18S/: .biom files for 18S data from Insect blends generated with variable thresholds as described in the manuscript.
• 1_AU_MOCK_biom_files_COI/: .biom files for COI data from Insect blends generated with variable thresholds as described in the manuscript.
• 2_ANT_SOIL_biom_18S/: .biom files for 18S data from Antarctic soils generated with variable thresholds as described in the manuscript.
• 2_ANT_SOIL_biom_COI/: .biom files for COI data from Antarctic soils generated with variable thresholds as described in the manuscript.
• 3_ANT_MORPH/: .biom files containing information from morphological assessments of Antarctic soil samples.
• 4_rep_sets/: compressed .fasta files containing relevant sequences for 18S and COI data sets (as indicated in file ./160121_file_collation_for_upload.txt).
• 5_mapping_files/: mapping files for raw data generation using Qiime. Note: Samples are filtered in shell scripts (.sh) and the main analysis file (160127_data_analysis_3.R).

Files

• ./160121_comparison_values.txt:
• ./160121_file_collation_for_upload.txt: extract of output from ./160127_data_analysis_3.Rdata; for writing.
• ./160121_Rplot_1.pdf: Raw R plot, used in manuscript or supplemental file, generated by./160127_data_analysis_3.R.
• ./160121_Rplot_2.pdf: Raw R plot, used in manuscript or supplemental file, generated by./160127_data_analysis_3.R.
• ./160121_Rplot_3.pdf: Raw R plot, used in manuscript or supplemental file, generated by./160127_data_analysis_3.R.
• ./160121_Rplot_4.pdf: Raw R plot, used in manuscript or supplemental file, generated by./160127_data_analysis_3.R.
• ./160122_Rplot_5.pdf: Raw R plot, used in manuscript or supplemental file, generated by./160127_data_analysis_3.R.
• ./160122_Rplot_6.pdf: Raw R plot, used in manuscript or supplemental file, generated by./160127_data_analysis_3.R.
• ./160122_Rplot_7.pdf: Raw R plot, used in manuscript or supplemental file, generated by./160127_data_analysis_3.R.
• ./160122_Rplot_8.pdf: Raw R plot, used in manuscript or supplemental file, generated by./160127_data_analysis_3.R.
• ./160122_Rplot_9.pdf: Raw R plot, used in manuscript or supplemental file, generated by./160127_data_analysis_3.R.
• ./160127_data_analysis_1a_18S.sh: Data preparation using bash and macqiime (18S). Do not execute this script without looking at it.
• ./160127_data_analysis_1b_COI.sh: Data preparation using bash and macqiime (COI). Do not execute this script without looking at it.
• ./160127_data_analysis_2.sh: Data preparation using bash and macqiime (18S and COI). Do not execute this script without looking at it.
• ./160127_data_analysis_3.R: Main analysis. Uses .biom files in this directory structure. Do not execute this script without looking at it.
• ./160127_data_analysis_3.Rdata: (May not be present). Copy of R environment after successful run of R analysis.
• ./160621_package_citations.bib: Citations for R packages, generated by./160127_data_analysis_3.R.
• ./README.md: This file.