bionic (1) pbalign.1.gz

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)