changed to MIT license
Added info about assembly and ortholog identification
added commands to blast Copci genes against the Augustus gene predictions
Added scripts to compare Exonerate/Augustus gene predictions to reference and to run Blobology
Added command to filter out short (<500 bp) contigs before blasting/mapping

When I tried this with all contigs, there were so many short ones that very few contigs
had blast matches
added FastQC quality reports for all datasets
added script to calculate the % gap characters in each sequence in an alignment
added info about all scripts, dependancies, and datasets
Added list markdown
Added markdown to make lists
Separate out Assembly step from annotation and ortholog identification so they can be run independently
add tests for existence of intermediary files so unnecessary steps don't need to be repeated

this is like a poor man's MAKE, but I've been struggling to get make to do what I want
added make files to run all steps automatically.

This is still a work in progress and hasn't been completely tested
added script to extract Copci seqs from folders
wrapped Augustus commands in file test to skip if already done

This is also something that would be better handled by a make file, but I'm somewhat
stuck with this for now, and this is a step that I don't want to rerun unless I have to
as it takes hours
added code to remove gap characters from the sequences
added code to create any missing directories
added script to translate Exonerate results and changed header formatting

I modified the ryo argument to Exonerate to format the header line of the fasta sequences
to be Species_jgi|Copci|gene_family

I also added my script for translating fasta sequences from STDIN and piped the Exonerate output
thru it
modified to add folder name to blast query
added the reference seqs to the prereqs for homolog extraction