Ancestral Reconstruction Pipeline

• Images from hackathon
• Notes on pipeline details

Plan for refactoring

GetGenomes: remove config file, add option to specify output dir for output files

• -d<directory of input synmap files>
• -g gid1,gid2,gid3,gid4... <list of common separated coge genome ids>
• -p p1,p2,p3,p4 <list of comma separated ploidy levels for genomes -- note these are paired ordered data with the -g option?>
• -s < subgenome_file>
• -o <output directory for SubGenomeInGeneOrder OrthologSets GenomeInString files>

GetContigInput

• Remove config file dependency
• -g gid1,gid2,gid3,gid4... <list of common separated coge genome ids>
• -w w1,w2,w3,w4 <list of comma separated weights for genomes -- note these are paired ordered data with the -g option?>
• -wa <threshold minimum adjacency score for keeping a contig. Called 'weightOfAdjacent' in original config file>
• -i <input file: GenomesInString from program GetGenomes>
• -o <output file name>

Note: Output is now a tab delimited file with each line containing: vertex vertex weight . These data will be used by the MEMPython data below

MWMPython: http://jorisvr.nl/maximummatching.html needs command line options for

• -i <input file or directory>
  • • File type is a set of vertex vertex weight
    • note: if directory, will batch process all files
• -o <outfile or directory> If no option is specified, the results go to STDOUT

GetContigOutputAndScaffoldInput

Note: goal is to get everything onto the command line. Currently, several of the files are hardcoded

• -cl <threshold minimum contig length. Called 'minimumGeneGroupLength' in original config file>
• -b <Number of bins for assignment to ancestral chromosomes. Called 'AncChrNumber' in original config file> (Note: this may be removed if this info can be derived from the input -- specifically the SubGenomesInGeneOrder file).)

Note: genomeInContigIndex is specified in the config file. This is the weighting for each subgenome. Need to discuss how best to deal with these.

• -co <configoutput file generated by the MWMPython program>
• -sg <subGenomesInGeneOrder file>
• -gf <genomeInString file>
• -o <output directory name>

Note: Output is a directory of tab delimited files with each line containing: vertex vertex weight . These data will be used by the MEMPython program Note: Multiple output files, one for each ancestral chromosome bin

MWMPython

Reuse of the same program listed above

ScaffoldOutput

• -i <directory of input files>
• -o <output file of reconstructed genome>