NAME

       pbalign - Mapping PacBio sequences to references

DESCRIPTION

       usage: pbalign [-h] [--version] [--log-file LOG_FILE]

              [--log-level  {DEBUG,INFO,WARNING,ERROR,CRITICAL} | --debug | --quiet | -v] [--pdb]
              [--regionTable  REGIONTABLE]  [--configFile  CONFIGFILE]  [--pulseFile   PULSEFILE]
              [--algorithm     {blasr,bowtie,gmap}]    [--maxHits    MAXHITS]    [--minAnchorSize
              MINANCHORSIZE]  [--maxMatch  MAXMATCH]  [--useccs  {useccs,useccsall,useccsdenovo}]
              [--noSplitSubreads]     [--concordant]    [--nproc    NPROC]    [--algorithmOptions
              ALGORITHMOPTIONS]  [--maxDivergence  MAXDIVERGENCE]   [--minAccuracy   MINACCURACY]
              [--minLength      MINLENGTH]      [--scoreCutoff      SCORECUTOFF]     [--hitPolicy
              {randombest,allbest,random,all,leftmost}]    [--filterAdapterOnly]     [--unaligned
              UNALIGNED]  [--seed SEED] [--tmpDir TMPDIR] [--profile] 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 can be in SAM or BAM format. If  output
       is  BAM  format, aligner can only be blasr and QVs will be loaded automatically. NOTE that
       pbalign no longer supports CMP.H5 in 3.0.

   positional arguments:
       inputFileName
              SubreadSet or unaligned .bam

       referencePath
              Reference DataSet or FASTA file

       outputFileName
              Alignment results dataset

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

       --version
              show program's version number and exit

       --log-file LOG_FILE
              Write the log to file. Default(None) will write to stdout. (default: None)

       --log-level {DEBUG,INFO,WARNING,ERROR,CRITICAL}
              Set log level (default: INFO)

       --debug
              Alias for setting log level to DEBUG (default: False)

       --quiet
              Alias for setting log level to CRITICAL to suppress output. (default: False)

       -v, --verbose
              Set the verbosity level. (default: None)

       --pdb  Enable Python debugger (default: False)

       --profile
              Print runtime profile at exit (default: False)

   Optional input arguments:
       --regionTable REGIONTABLE
              Specify a region table for filtering reads. (default: None)

       --configFile CONFIGFILE
              Specify a set of user-defined argument values.  (default: None)

       --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.
              (default: None)

   Alignment options:
       --algorithm {blasr,bowtie,gmap}
              Select an aligorithm from ('blasr', 'bowtie', 'gmap').  (default: blasr)

       --maxHits MAXHITS
              The maximum number of matches of each read to the reference sequence that  will  be
              evaluated. (default: None)

       --minAnchorSize MINANCHORSIZE
              The  minimum anchor size defines the length of the read that must match against the
              reference sequence.  (default: None)

       --maxMatch MAXMATCH
              BLASR maxMatch option. (Will be overriden  if  is  also  set  in  algorithmOptions)
              (default: 30)

       --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. (default:
              None)

       --noSplitSubreads
              Do not split reads into subreads even if subread regions are  available.  (default:
              False)

       --concordant
              Map subreads of a ZMW to the same genomic location.  (default: False)

       --nproc NPROC
              Number of threads. (default: 8)

       --algorithmOptions ALGORITHMOPTIONS
              Pass alignment options through. (default: None)

   Filter criteria options:
       --maxDivergence MAXDIVERGENCE
              The  maximum  allowed  percentage divergence of a read from the reference sequence.
              (default: 30.0)

       --minAccuracy MINACCURACY
              The minimum concordance of alignments that will be evaluated. (default: 70.0)

       --minLength MINLENGTH
              The minimum aligned read length of alignments that will be evaluated. (default: 50)

       --scoreCutoff SCORECUTOFF
              The worst score to output an alignment. (default: None)

       --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: randombest)

       --filterAdapterOnly
              If  specified, do not report adapter-only hits using annotations with the reference
              entry. (default: False)

   Miscellaneous options:
       --unaligned UNALIGNED
              Output names of unaligned reads to specified file.  (default: None)

       --seed SEED
              Initialize the random number generator with a nonezero  integer.  Zero  means  that
              current system time is used. (default: 1)

       --tmpDir TMPDIR
              Specify a directory for saving temporary files.  (default: /tmp)