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.

pbalign 0.2.0                                    September 2015                                       PBALIGN(1)