Ancestral Reconstruction Pipeline

Pipeline

Refactored pipeline

• Images from hackathon
• Notes on pipeline details

Plan for refactoring

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

This program gets data ready for downstream processing

• -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

This program gets data ready for ancestral ordering of genes by MWM

• 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

This program is a general tool for Maximum Weight Matching. First run is for ancestral gene ordering. Second run is for ancestral contig ordering

• -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

This program maps ancestral contigs back to various genomes, gets their positions, and gets data formatted for a second MWM to generate ancestral ordered contigs Note: goal is to get everything onto the command line. Currently, several of the files are hardcoded

• -mml <threshold minimum mapping length. The minimum number of "genes" mapping to a subgenome. Called 'minimumGeneGroupLength' in original config file>

Note: genomeInContigIndex is specified in the config file. This is the weighting for each subgenome. These values will be removed and the weights for genomes used instead:

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

Note: Multiple output files, one for each ancestral chromosome bin

Note: There are three sets of data that are needed for the subsequent steps:

• Directory named "scaffolds". These tab delimited files with each line containing: vertex vertex weight. These data will be used by the MEMPython program
• Directory named "binfiles". These files are used in the final program ScaffoldOutput to assign the correct contigs to the bins
• File named "contig2genes.txt"

MWMPython

Reuse of the same program listed above for ancestral ordering of contigs

ScaffoldOutput

Putting all the output data back together for the final ancestral genome

• -im <directory of MWM files>
• -ib <directory composition of bin files>
• -cg <file containing the looking up of gene families comprising contigs
• -o <output file of reconstructed genome>