PBALIGN

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)