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BLASR(1) User Commands BLASR(1)


blasr - Map SMRT Sequences to a reference genome


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

blasr reads.fasta genome.fasta

blasr reads.fasta genome.fasta --sa

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

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

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


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 quality 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 to bax.h5 and plx.h5 files will be DEPRECATED. Support to 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, and then specify the suffix array on the command line using -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.


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

January 2019 blasr 5.3.2