SQLite used for the database.

get_ncbi_files.py uses Biopython to query NCBI by species name and download the files.

You will need to supply your email and NCBI API key (see https://www.ncbi.nlm.nih.gov/home/develop/api/)

You will also need to supply the preferred download directory for the genome files.

Ortholog calling with OrthoFinder. Version of Orthofinder on Hal: 2.51 Version of Orthofinder on Cluster: 2.4

MAFFT v7.149b (2014/04/04) http://mafft.cbrc.jp/alignment/software/ MBE 30:772-780 (2013), NAR 30:3059-3066 (2002)

• Check to see if there's a better way to do this filter.
• Can use a method to eliminate badly aligned regions of the genes.

trees: IQ-Tree

Species tree is a literature synthesis from the Open Tree of Life project with undated nodes dated through a literature search.

• Check to see if there is data about any of these plants other than Arabidopsis thaliana. May need to restrict only to trees that contain Arabidopsis thaliana genes (honestly, I wouldn't mind some restriction...)

• There are multiple species that have GO calls on geneontology.org

###parallel-fastq-dump : 0.6.7

fastq-dump : 2.8.0 Downloaded the SRR files for each experiment using parallel-fastq-dump https://github.com/rvalieris/parallel-fastq-dump

###FastQC v0.11.5 Ran before and after trimming.

Checked for the contaminants listed her: https://github.com/csf-ngs/fastqc/blob/master/Contaminants/contaminant_list.txt

Combined all fastqc results into a single .html file using this script: https://github.com/riverlee/CQScripts/blob/master/merge_fastqc_report.pl

fastp: an ultra-fast all-in-one FASTQ preprocessor version 0.12.4

Platforms used in these studies: Illumina HiSeq 2000 Illumina Genome Analyzer Illumina Genome Analyzer IIx Illumina MiSeq NextSeq 500 Illumina HiSeq 4000 HiSeq X Ten Illumina HiSeq 2500