Provided by: blasr_5.3+0-2_amd64 bug

NAME

       blasr - Map SMRT Sequences to a reference genome.

SYNOPSIS

       blasr reads.bam genome.fasta -bam -out out.bam

       blasr reads.fasta genome.fasta

       blasr reads.fasta genome.fasta -sa genome.fasta.sa

       blasr reads.bax.h5 genome.fasta [-sa genome.fasta.sa]

       blasr reads.bax.h5 genome.fasta -sa genome.fasta.sa -maxScore -100 -minMatch 15 ...

       blasr reads.bax.h5 genome.fasta -sa genome.fasta.sa -nproc 24 -out alignment.out ...

DESCRIPTION

       blasr  is  a  read  mapping program that maps reads to positions in a genome by clustering
       short exact matches between the read and the genome, and scoring clusters using alignment.
       The  matches  are generated by searching all suffixes of a read against the genome using a
       suffix array. Global chaining methods are used to score clusters of matches.

       The only required inputs to blasr are a file of reads  and  a  reference  genome.   It  is
       exremely  useful  to  have  read  filtering  information, and mapping runtime may decrease
       substantially when  a  precomputed  suffix  array  index  on  the  reference  sequence  is
       specified.

       Although  reads  may  be  input in FASTA format, the recommended input is PacBio BAM files
       because these contain qualtiy value information that is used in the alignment and produces
       higher  quality  variant detection.  Although alignments can be output in various formats,
       the recommended output format is PacBio BAM.  Support for bax.h5 and plx.h5 files will  be
       DEPRECATED.  Support for region tables for h5 files will be DEPRECATED.

       When  suffix  array  index  of a genome is not specified, the suffix array is built before
       producing alignment. This may be prohibitively slow when the genome is large (e.g. Human).
       It  is  best to precompute the suffix array of a genome using the program sawriter(1), and
       then specify the suffix array on the command line using -sa genome.fa.sa.

       The optional parameters are roughly divided into three categories: control over anchoring,
       alignment scoring, and output.

       The  default  anchoring parameters are optimal for small genomes and samples with up to 5%
       divergence from the reference genome.  The main parameter governing speed and  sensitivity
       is  the  -minMatch  parameter.   For  human  genome alignments, a value of 11 or higher is
       recommended.  Several methods may be used to  speed  up  alignments,  at  the  expense  of
       possibly decreasing sensitivity.

       Regions  that  are  too repetitive may be ignored during mapping by limiting the number of
       positions a read maps to with the -maxAnchorsPerPosition option. Values  between  500  and
       1000 are effective in the human genome.

       For small genomes such as bacterial genomes or BACs, the default parameters are sufficient
       for maximal sensitivity and good speed.

OPTIONS

       Input Files

              Reads

                     reads.bam
                            A PacBio BAM file of reads.  This is the  preferred  input  to  blasr
                            because  rich  quality  value  (insertion,deletion,  and substitution
                            quality  values)  information  is  maintained.   The  extra   quality
                            information improves variant detection and mapping speed.

                     reads.fasta
                            A multi-fasta file of reads, though any fasta file is valid input

                     reads.bax.h5|reads.plx.h5
                            the old DEPRECATED output format of SMRT reads.

                     input.fofn
                            File of file names

              -sa suffixArrayFile
                     Use  the  suffix  array 'sa' for detecting matches between the reads and the
                     reference.  The suffix array has been prepared by the sawriter(1) program.

              -ctab tab
                     A table of tuple counts used to estimate match significance.  This is by the
                     program  'printTupleCountTable'.   While it is quick to generate on the fly,
                     if there are many invocations of blasr, it is useful to precompute the ctab.

              -regionTable table (DEPRECATED)
                     Read in a read-region table in HDF format for  masking  portions  of  reads.
                     This may be a single table if there is just one input file, or a fofn.  When
                     a region table is specified, any region table  inside  the  reads.plx.h5  or
                     reads.bax.h5 files are ignored.
       (DEPRECATED) Options for modifying reads.

              There  is  ancilliary  information  about  substrings  of reads that is stored in a
              'region table' for each read file.  Because HDF is used, the region  table  may  be
              part  of  the  .bax.h5  or  .plx.h5  file, or a separate file.  A contiguously read
              substring from the template is  a  subread,  and  any  read  may  contain  multiple
              subreads.  The  boundaries  of  the  subreads may be inferred from the region table
              either directly or by definition of adapter boundaries.   Typically  region  tables
              also  contain  information  for the location of the high and low quality regions of
              reads.  Reads produced by spurious reads from empty ZMWs have a high quality  start
              coordinate equal to high quality end, making no usable read.

              -useccs
                     Align  the  circular consensus sequence (ccs), then report alignments of the
                     ccs subreads to the window that the ccs was mapped to.  Only  alignments  of
                     the subreads are reported.

              -useccsall
                     Similar  to  -useccs,  except all subreads are aligned, rather than just the
                     subreads used to call the ccs.  This will include reads that only cover part
                     of the template.

              -useccsdenovo
                     Align  the  circular  consensus,  and  report  only the alignment of the ccs
                     sequence.

              -noSplitSubreads (false)
                     Do not split subreads at adapters. This is typically only  useful  when  the
                     genome  in  an  unrolled version of a known template, and contains template-
                     adapter-reverse_template sequence.

              -ignoreRegions (false)
                     Ignore any information in the region table.

              -ignoreHQRegions (false)
                     Ignore any hq regions in the region table.
       Alignments To Report

              -bestn n (10)
                     Report the top n alignments.

              -hitPolicy (all)
                     Specify a  policy  to  treat  multiple  hits  from  [all,  allbest,  random,
                     randombest, leftmost]

                     all    report all alignments.

                     allbest
                            report all equally top scoring alignments.

                     random report a random alignment.

                     randombest
                            report   a   random  alignment  from  multiple  equally  top  scoring
                            alignments.

                     leftmost
                            report an alignment which has the best  alignmentscore  and  has  the
                            smallest mapping coordinate in any reference.

              -placeRepeatsRandomly (false)
                     DEPRECATED! If true, equivalent to -hitPolicy randombest.

              -randomSeed (0)
                     Seed for random number generator. By default (0), use current time as seed.

              -noSortRefinedAlignments (false)
                     Once  candidate  alignments  are  generated  and  scored  via sparse dynamic
                     programming, they are rescored  using  local  alignment  that  accounts  for
                     different error profiles.  Resorting based on the local alignment may change
                     the order the hits are returned.

              -allowAdjacentIndels
                     When specified, adjacent insertion  or  deletions  are  allowed.  Otherwise,
                     adjacent  insertion  and  deletions  are  merged  into one operation.  Using
                     quality values to guide pairwise alignments  may  dictate  that  the  higher
                     probability  alignment  contains  adjacent insertions or deletions.  Current
                     tools such as GATK do not permit this  and  so  they  are  not  reported  by
                     default.
       Output Formats and Files

              -out out (terminal)
                     Write output to out.

              -sam   Write output in SAM format.

              -m t   If not printing SAM, modify the output of the alignment.

              When t is:

                     0      Print blast like output with |'s connecting matched nucleotides.

                     1      Print only a summary: score and pos.

                     2      Print in Compare.xml format.

                     3      Print in vulgar format (DEPRECATED).

                     4      Print a longer tabular version of the alignment.

                     5      Print    in    a    machine-parsable   format   that   is   read   by
                            compareSequences.py.

              -header
                     Print a header as the first line of the output file describing the  contents
                     of each column.

              -titleTable tab (NULL)
                     Construct a table of reference sequence titles.  The reference sequences are
                     enumerated by row, 0,1,...  The reference  index  is  printed  in  alignment
                     results  rather  than  the  full reference name.  This makes output concise,
                     particularly whenvery verbose titles exist in reference names.

              -unaligned file
                     Output reads that are not aligned to file

              -clipping [none|hard|subread|soft] (none)

                     Use no/hard/subread/soft clipping, ONLY for SAM/BAM output.

              -printSAMQV (false)
                     Print quality values to SAM output.

              -cigarUseSeqMatch (false)
                     CIGAR strings in SAM/BAM output use '=' and 'X' to represent sequence  match
                     and mismatch instead of 'M'.
       Options for anchoring alignment regions.

              This will have the greatest effect on speed and sensitivity.

              -minMatch m (12)
                     Minimum  seed length.  Higher minMatch will speed up alignment, but decrease
                     sensitivity.

              -maxMatch l (inf)
                     Stop mapping a read to the genome when the lcp length reaches  l.   This  is
                     useful   when  the  query  is  part  of  the  reference,  for  example  when
                     constructing pairwise alignments for de novo assembly.

              -maxLCPLength l (inf)
                     The same as -maxMatch.

              -maxAnchorsPerPosition m (10000)
                     Do not add anchors from a position if it matches to more than m locations in
                     the target.

              -advanceExactMatches E (0)
                     Another  trick  for  speeding  up  alignments  with match - E fewer anchors.
                     Rather than finding anchors  between  the  read  and  the  genome  at  every
                     position  in  the  read,  when an anchor is found at position i in a read of
                     length L, the next position in a read to find an anchor is  at  i+L-E.   Use
                     this when alignining already assembled contigs.

              -nCandidates n (10)
                     Keep  up  to  n  candidates for the best alignment.  A large value of n will
                     slow mapping because the slower dynamic programming  steps  are  applied  to
                     more  clusters  of  anchors which can be a rate limiting step when reads are
                     very long.

              -concordant (false)
                     Map all subreads of a zmw (hole) to where the longest full pass  subread  of
                     the  zmw  aligned  to. This requires to use the region table and hq regions.
                     This option only works when reads are in base or pulse h5 format.

              -concordantTemplate (mediansubread)
                     Select a full pass subread of a zmw  as  template  for  concordant  mapping.
                     longestsubread  - use the longest full pass subread mediansubread  - use the
                     median length full pass subread typicalsubread - use the second longest full
                     pass subread if length of the longest full pass subread is an outlier

              -fastMaxInterval (false)
                     Fast search maximum increasing intervals as alignment candidates. The search
                     is not as exhaustive as the default, but is much faster.

              -aggressiveIntervalCut (false)
                     Agreesively filter out non-promising alignment candidates, if  there  exists
                     at  least  one  promising  candidate.  If this option is turned on, blasr is
                     likely to ignore short alignments of ALU elements.

              -fastSDP (false)
                     Use a fast heuristic algorithm to speed up sparse dynamic programming.
       Options for Refining Hits

              -sdpTupleSize K (11)
                     Use matches of length K  to  speed  dynamic  programming  alignments.   This
                     controls  accuracy  of  assigning gaps in pairwise alignments once a mapping
                     has been found, rather than mapping sensitivity itself.

              -scoreMatrix score matrix string
                     Specify an alternative score matrix for scoring fasta reads.  The matrix  is
                     in the format

                       A C G T N
                     A a b c d e
                     C f g h i j
                     G k l m n o
                     T p q r s t
                     N u v w x y

                     The  values a...y should be input as a quoted space separated string: "a b c
                     ... y". Lowerf scores are better, so matches should be less than  mismatches
                     e.g. a,g,m,s = -5 (match), mismatch = 6.

              -affineOpen value (10)
                     Set the penalty for opening an affine alignment.

              -affineExtend a (0)
                     Change affine (extension) gap penalty. Lower value allows more gaps.
       Options  for  overlap/dynamic  programming  alignments  and  pairwise  overlap for de novo
       assembly.

              -useQuality (false)
                     Use substitution/insertion/deletion/merge quality values to  score  gap  and
                     mismatch  penalties  in  pairwise  alignments.  Because  the  insertion  and
                     deletion rates are much  higher  than  substitution,  this  will  make  many
                     alignments  favor an insertion/deletion over a substitution.nNaive consensus
                     calling methods will then often miss substitution polymorphisms. This option
                     should  be used when calling consensus using the Quiver method. Furthermore,
                     when not using quality values to score alignments, there  will  be  a  lower
                     consensus accuracy in homolymer regions.

              -affineAlign (false)
                     Refine alignment using affine guided align.
       Options for filtering reads and alignments

              -minReadLength l (50)
                     Skip reads that have a full length less than l. Subreads may be shorter.

              -minSubreadLength l (0)
                     Do not align subreads of length less than l.

              -minRawSubreadScore m (0)
                     Do  not  align  subreads  whose quality score in region table is less than m
                     (quality scores should be in range [0, 1000]).

              -maxScore m (-200)
                     Maximum score to output (high is bad, negative good).

              -minAlnLength
                     (0) Report alignments only if their lengths are greater than minAlnLength.

              -minPctSimilarity (0) Report alignments only  if  their  percentage  similairty  is
                     greater than minPctSimilarity.

              -minPctAccuracy
                     (0)  Report  alignments  only  if  their  percentage accuray is greater than
                     minAccuracy.
       Options for parallel alignment

              -nproc N (1)
                     Align using N processes. All large data structures such as the suffix  array
                     and tuple count table are shared.

              -start S (0)
                     Index  of  the  first  read to begin aligning.  This is useful when multiple
                     instances are running on the same data, for example  when  on  a  multi-rack
                     cluster.

              -stride S (1)
                     Align one read every S reads.
       Options for subsampling reads.

              -subsample (0)
                     Proportion  of  reads  to  randomly  subsample  (expressed as a decimal) and
                     align.

              -holeNumbers LIST
                     When specified, only align reads whose ZMW hole numbers are in  LIST.   LIST
                     is  a  comma-delimited string of ranges, such as '1,2,3,10-13'.  This option
                     only works when reads are in bam, bax.h5 or plx.h5 format.

       -h     Print help information.

CITATION

       To cite BLASR,  please  use:  Chaisson  M.J.,  and  Tesler  G.,  Mapping  single  molecule
       sequencing  reads  using  Basic Local Alignment with Successive Refinement (BLASR): Theory
       and Application, BMC Bioinformatics 2012, 13:238.

BUGS

       Please report any bugs to https://github.com/PacificBiosciences/blasr/issues.

SEE ALSO

       loadPulses(1) pls2fasta(1) samFilter(1) samtoh5(1)  samtom4(1)  sawriter(1)  sdpMatcher(1)
       toAfg(1)