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- buster 0.3.2-1
| PBALIGN(1) | User Commands | PBALIGN(1) |
NAME¶
pbalign - Mapping PacBio sequences to referencesDESCRIPTION¶
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.| October 2018 | pbalign 0.3.1 |