Directory.txt

Align.py 	
 - simple SW implementation
Align.pyc																 
AlignConsensus.py
 - Align quiver output to the genome, and find gaps.
AnnotateCoverage.py
  - print FLAG/ok 											 
AnnotateGapBed.py
  - Given a gapped bed file and repeat masker output for the gap sequences, add the annotations from the repeatmasker .out file to this the bed table.
AssembleRegion.sh												 
AssembleRegions.sh												 
BinBPCoords.py
  - Find clusters of breakpoints with split reads.
BlasrSelfAlign.py
  				 
BlasrSelfAlign.sh 	
BreakpointCluster.py 										 
BuildConsensus.mak 	
CheckInvTests.py 												 
ClassifyRepeats.py 	
ComputeCloneSize.py 	
CountRestrictionSites.py 	
DetectInversions.mak 	
DetectInversions.py											 
DotPlot.py
  - Tool to dot plot two sequences, with many options.								 
ExtractSeq.py 	   
  - Using a .fai file, extract a fasta sequence
FastBPCluster.py 		
  - Cluster two sided breakpoints.																	
FastBreakpointCluster.py  
  - Not sure why this second one exists.	
FastaToFakeFastq.py 	 
  - Generate a fastq suitable for Celera assembly input.												FilterGaps.py 	 
  - Filter gaps based on ratio of gap coverage to local genomic coverage.
FilterHPGaps.py 	 
  - A lot of false positive gaps in PacBio reads are homopolymers.  This can filter them out.
FilterSupport.py 	
FilterUniqueReads.py 	
FindBasFiles.py 	
FindJoined.py														 
FindL1NearAlignments.py									 
FindL1NearHardStops.py										 
FindPairedSupport.py											 
GC_content_explore.py										 
GapBedToFasta.py													 
GapSupportToFasta.py											 
GetReadsInRegion.sh											 
InSilicoDigest.py												 
InsertionBedToConsensus.py								 
MakeNameQuery.py 	
MergeBed.py 	
MergeGapSupport.py 	
Overloading.py 	
PickFirstCovEntry.py 	
PickSeedRead.py 	
PlotFrequency.py 	
PlotSubreadHist.py 	

PrintAssemblies.py
  . Print the Celera assembly rgn_*/region/9-terminator/region.ctg.fasta

PrintBedFlank.py 	
  . Print a window of either the left side or right side of a bed interval.
PrintBinAverage.py 	
PrintBrokenAlignmets.py 	
PrintChunkedGenomeRegions.py 	
  . Print a number of regions from a genome
PrintDisjointSplits.py 	
PrintFastaGroups.py											 
PrintFrequency.py												 
PrintGapSupport.py												 
PrintGaps.optimize.py										 
PrintGaps.py															 
PrintHardStop.py													 
PrintReadsInRegion.csh										 
PrintSAMSubset.py												 
PrintSplitAlignmentCoordinates.py				 
PrintSupportIdentity.py									 
PrintTruncatedAlignments.py
PrintUniqueReadSupport.py								 
QueryNameListWithM1.py										 
QuickDotPlot.py													 
QuiverRegion.py 	
R-plot_commands.txt 	
RegionToFasta.py 	
ReorderClusters.py 	
ResultsTableToGraph.py 	
RunDotPlots.csh 	
RunDotPlots.py 	
SamCons.py 	
SamToBed.py 	
SamToFasta.py 	
SearchDeletions.cpp 	
SummarizeFromAlignments.py 	
TakeTopHitFromSAM.py 	
TitlesToFileIndex.py											 
Tools.py																	 
Tools.pyc 	
TopHitOnly.py 	
awk_commands.txt