NAME

       pbalign - Mapping PacBio sequences to references

DESCRIPTION

       usage: pbalign [-h] [--verbose] [--version] [--profile] [--debug]

              [--regionTable   REGIONTABLE]  [--configFile  CONFIGFILE]  [--pulseFile  PULSEFILE]
              [--algorithm    {blasr,bowtie,gmap}]    [--maxHits    MAXHITS]     [--minAnchorSize
              MINANCHORSIZE]   [--useccs   {useccs,useccsall,useccsdenovo}]   [--noSplitSubreads]
              [--concordant]    [--nproc     NPROC]     [--algorithmOptions     ALGORITHMOPTIONS]
              [--maxDivergence MAXDIVERGENCE] [--minAccuracy MINACCURACY] [--minLength MINLENGTH]
              [--scoreFunction  {alignerscore,editdist,blasrscore}]  [--scoreCutoff  SCORECUTOFF]
              [--hitPolicy     {randombest,allbest,random,all,leftmost}]    [--filterAdapterOnly]
              [--forQuiver] [--loadQVs] [--byread] [--metrics METRICS]  [--seed  SEED]  [--tmpDir
              TMPDIR] inputFileName referencePath outputFileName

       Mapping  PacBio  sequences  to  references using an algorithm selected from a selection of
       supported command-line alignment algorithms. Input can  be  a  fasta,  pls.h5,  bas.h5  or
       ccs.h5 file or a fofn (file of file names). Output is in either cmp.h5 or sam format.

   positional arguments:
       inputFileName
              The input file can be a fasta, plx.h5, bax.h5, ccs.h5 file or a fofn.

       referencePath
              Either a reference fasta file or a reference repository.

       outputFileName
              The output cmp.h5 or sam file.

   optional arguments:
       -h, --help
              show this help message and exit

       --verbose, -v
              Set the verbosity level

       --version
              show program's version number and exit

       --profile
              Print runtime profile at exit

       --debug
              Catch exceptions in debugger (requires ipdb)

       --regionTable REGIONTABLE
              Specify a region table for filtering reads.

       --configFile CONFIGFILE
              Specify a set of user-defined argument values.

       --pulseFile PULSEFILE
              When input reads are in fasta format and output is a cmp.h5 this option can specify
              pls.h5 or bas.h5 or FOFN files from which pulse metrics can be loaded for Quiver.

       --algorithm {blasr,bowtie,gmap}
              Select an aligorithm from ('blasr', 'bowtie', 'gmap').  Default algorithm is blasr.

       --maxHits MAXHITS
              The maximum number of matches of each read to the reference sequence that  will  be
              evaluated. Default value is 10.

       --minAnchorSize MINANCHORSIZE
              The  minimum anchor size defines the length of the read that must match against the
              reference sequence. Default value is 12.

       --useccs {useccs,useccsall,useccsdenovo}
              Map the ccsSequence to the genome first, then align subreads to the  interval  that
              the CCS reads mapped to.

       useccs: only maps subreads that span the length of
              the template.

       useccsall: maps all subreads.
              useccsdenovo: maps ccs only.

       --noSplitSubreads
              Do  not  split  reads  into subreads even if subread regions are available. Default
              value is False.

       --concordant
              Map subreads of a ZMW to the same genomic location.

       --nproc NPROC
              Number of threads. Default value is 8.

       --algorithmOptions ALGORITHMOPTIONS
              Pass alignment options through.

       --maxDivergence MAXDIVERGENCE
              The maximum allowed percentage divergence of a read from  the  reference  sequence.
              Default value is 30.

       --minAccuracy MINACCURACY
              The minimum percentage accuracy of alignments that will be evaluated. Default value
              is 70.

       --minLength MINLENGTH
              The minimum aligned read length of alignments that will be evaluated. Default value
              is 50.

       --scoreFunction {alignerscore,editdist,blasrscore}
              Specify a score function for evaluating alignments.

       alignerscore : aligner's score in the SAM tag 'as'.
              editdist      :  edit  distance between read and reference.  blasrscore   : blasr's
              default score function.

              Default value is alignerscore.

       --scoreCutoff SCORECUTOFF
              The worst score to output an alignment.

       --hitPolicy {randombest,allbest,random,all,leftmost}
              Specify a policy for how to treat multiple hit

       random : selects a random hit.

       all    : selects all hits.

       allbest
              : selects all the best score hits.

       randombest: selects a random hit from all best score hits.
              leftmost  : selects a hit which has the best score and the

       smallest mapping coordinate in any reference.
              Default value is randombest.

       --filterAdapterOnly
              If specified, do not report adapter-only hits using annotations with the  reference
              entry.

       --forQuiver
              The  output cmp.h5 file which will be sorted, loaded with pulse QV information, and
              repacked, so that it can be consumed by quiver directly. This  requires  the  input
              file to be in PacBio bas/pls.h5 format, and --useccs must be None. Default value is
              False.

       --loadQVs
              Similar to --forQuiver, the only difference is  that  --useccs  can  be  specified.
              Default value is False.

       --byread
              Load  pulse  information using -byread option instead of -bymetric. Only works when
              --forQuiver or --loadQVs are set. Default value is False.

       --metrics METRICS
              Load the specified (comma-delimited list of) metrics instead of the default metrics
              required by quiver.  This option only works when --forQuiver  or --loadQVs are set.
              Default: DeletionQV,DeletionTag,InsertionQV,MergeQV,SubstitutionQV

       --seed SEED
              Initialize the random number generator with a none-zero integer.  Zero  means  that
              current system time is used.  Default value is 1.

       --tmpDir TMPDIR
              Specify a directory for saving temporary files.  Default is /scratch.