.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.8.
.TH PBALIGN "1" "October 2018" "pbalign 0.3.1" "User Commands"
.SH NAME
pbalign \- Mapping PacBio sequences to references
.SH DESCRIPTION
usage: pbalign [\-h] [\-\-version] [\-\-log\-file LOG_FILE]
.IP
[\-\-log\-level {DEBUG,INFO,WARNING,ERROR,CRITICAL} | \fB\-\-debug\fR | \fB\-\-quiet\fR | \fB\-v]\fR
[\-\-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
.PP
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.
.SS "positional arguments:"
.TP
inputFileName
SubreadSet or unaligned .bam
.TP
referencePath
Reference DataSet or FASTA file
.TP
outputFileName
Alignment results dataset
.SS "optional arguments:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.TP
\fB\-\-version\fR
show program's version number and exit
.TP
\fB\-\-log\-file\fR LOG_FILE
Write the log to file. Default(None) will write to
stdout. (default: None)
.TP
\fB\-\-log\-level\fR {DEBUG,INFO,WARNING,ERROR,CRITICAL}
Set log level (default: INFO)
.TP
\fB\-\-debug\fR
Alias for setting log level to DEBUG (default: False)
.TP
\fB\-\-quiet\fR
Alias for setting log level to CRITICAL to suppress
output. (default: False)
.TP
\fB\-v\fR, \fB\-\-verbose\fR
Set the verbosity level. (default: None)
.TP
\fB\-\-pdb\fR
Enable Python debugger (default: False)
.TP
\fB\-\-profile\fR
Print runtime profile at exit (default: False)
.SS "Optional input arguments:"
.TP
\fB\-\-regionTable\fR REGIONTABLE
Specify a region table for filtering reads. (default:
None)
.TP
\fB\-\-configFile\fR CONFIGFILE
Specify a set of user\-defined argument values.
(default: None)
.TP
\fB\-\-pulseFile\fR 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)
.SS "Alignment options:"
.TP
\fB\-\-algorithm\fR {blasr,bowtie,gmap}
Select an aligorithm from ('blasr', 'bowtie', 'gmap').
(default: blasr)
.TP
\fB\-\-maxHits\fR MAXHITS
The maximum number of matches of each read to the
reference sequence that will be evaluated. (default:
None)
.TP
\fB\-\-minAnchorSize\fR MINANCHORSIZE
The minimum anchor size defines the length of the read
that must match against the reference sequence.
(default: None)
.TP
\fB\-\-maxMatch\fR MAXMATCH
BLASR maxMatch option. (Will be overridden if is also
set in algorithmOptions) (default: 30)
.TP
\fB\-\-useccs\fR {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)
.TP
\fB\-\-noSplitSubreads\fR
Do not split reads into subreads even if subread
regions are available. (default: False)
.TP
\fB\-\-concordant\fR
Map subreads of a ZMW to the same genomic location.
(default: False)
.TP
\fB\-\-nproc\fR NPROC
Number of threads. (default: 8)
.TP
\fB\-\-algorithmOptions\fR ALGORITHMOPTIONS
Pass alignment options through. (default: None)
.SS "Filter criteria options:"
.TP
\fB\-\-maxDivergence\fR MAXDIVERGENCE
The maximum allowed percentage divergence of a read
from the reference sequence. (default: 30.0)
.TP
\fB\-\-minAccuracy\fR MINACCURACY
The minimum concordance of alignments that will be
evaluated. (default: 70.0)
.TP
\fB\-\-minLength\fR MINLENGTH
The minimum aligned read length of alignments that
will be evaluated. (default: 50)
.TP
\fB\-\-scoreCutoff\fR SCORECUTOFF
The worst score to output an alignment. (default:
None)
.TP
\fB\-\-hitPolicy\fR {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)
.TP
\fB\-\-filterAdapterOnly\fR
If specified, do not report adapter\-only hits using
annotations with the reference entry. (default: False)
.SS "Miscellaneous options:"
.TP
\fB\-\-unaligned\fR UNALIGNED
Output names of unaligned reads to specified file.
(default: None)
.TP
\fB\-\-seed\fR SEED
Initialize the random number generator with a nonezero integer. Zero means that current system time is
used. (default: 1)
.TP
\fB\-\-tmpDir\fR TMPDIR
Specify a directory for saving temporary files.
(default: \fI\,/tmp\/\fP)
.SH AUTHOR
This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.