---
name: "pbalign"
section: "1"
platform: "linux"
package: "pbalign"
version: "0.3.2-1"
release: "Debian 10 (Buster)"
platforms: ["linux"]
url: "https://new.carta.tech/pbalign"
---

# pbalign(1)

Mapping PacBio sequences to references

## 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 overridden 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*)

## AUTHOR

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.