version=2.4.2
pipeline=Single-cell
rootDir=/global/projectb/scratch/copeland/Projects/2014/20140214-ViralParticle-GAA691/ZHYY
finalQdReport=final/QD.finalReport.txt
spadesStats=spades/stats.spades
spadesContigsFile=spades/contigs.2k.fasta
spadesScaffoldsFile=spades/scaffolds.2k.fasta
finalAssemblyFile=spades/scaffolds.2k.fasta
finalAssemblyAgpFile=spades/submission.agp
finalAssemblyFileUnscreen=spades/scaffolds.2k.fasta
finalAssemblyAgpFileUnscreen=spades/submission.agp
finalContigGcPlot=contig_gc/contig_gc.png
finalContigGcHist=contig_gc/contig_gc.hist
finalContigGcWHist=contig_gc/contig_gc.whist
finalContigGcCsv=contig_gc/contig_gc.csv
meganContigKingdomPlot=megan/contigs_Kingdom.png
meganContigPhylumPlot=megan/contigs_Phylum.png
meganContigClassPlot=megan/contigs_Class.png
meganContigOrderPlot=megan/contigs_Order.png
meganContigFamilyPlot=megan/contigs_Family.png
meganContigGenusPlot=megan/contigs_Genus.png
meganContigSpeciesPlot=megan/contigs_Species.png
meganContigKingdomNoTotalPlot=megan/contigs_nototal_Kingdom.png
meganContigPhylumNoTotalPlot=megan/contigs_nototal_Phylum.png
meganContigClassNoTotalPlot=megan/contigs_nototal_Class.png
meganContigOrderNoTotalPlot=megan/contigs_nototal_Order.png
meganContigFamilyNoTotalPlot=megan/contigs_nototal_Family.png
meganContigGenusNoTotalPlot=megan/contigs_nototal_Genus.png
meganContigSpeciesNoTotalPlot=megan/contigs_nototal_Species.png
gcCovTaxKingdomPlot=gc_cov/gc_cov_Kingdom.png
gcCovTaxPhylumPlot=gc_cov/gc_cov_Phylum.png
gcCovTaxClassPlot=gc_cov/gc_cov_Class.png
gcCovTaxOrderPlot=gc_cov/gc_cov_Order.png
gcCovTaxFamilyPlot=gc_cov/gc_cov_Family.png
gcCovTaxGenusPlot=gc_cov/gc_cov_Genus.png
gcCovTaxSpeciesPlot=gc_cov/gc_cov_Species.png
gcCovTaxScaffold=gc_cov/cov/scaffolds_2k_gc_cov_nolegend.png
singleCopyGeneSummaryFileBacteria=single_copy_gene/bacteria/summary.bacteria.txt
singleCopyGeneGeneFileBacteria=single_copy_gene/bacteria/singleCopyGeneList.bacteria.txt
singleCopyGeneGenePlotBacteria=single_copy_gene/bacteria/genes.pdf
singleCopyGeneHistPlotBacteria=single_copy_gene/bacteria/hist.png
singleCopyGeneOutliersPlotBacteria=single_copy_gene/bacteria/outliers.png
singleCopyGeneSummaryFileArchaea=single_copy_gene/archaea/summary.archaea.txt
singleCopyGeneGeneFileArchaea=single_copy_gene/archaea/singleCopyGeneList.archaea.txt
singleCopyGeneGenePlotArchaea=single_copy_gene/archaea/genes.pdf
singleCopyGeneHistPlotArchaea=single_copy_gene/archaea/hist.png
singleCopyGeneOutliersPlotArchaea=single_copy_gene/archaea/outliers.png
jigsawStatsFile=jigsaw_stats.yaml