blasr1
Map smrt sequences to a reference genome
Usage
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 ...
Overview
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 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.
Releases
5 releases since Debian 9 (Stretch); the text changed 1 time.
-affineAlign until Debian 9 (Stretch);
-aggressiveIntervalCut until Debian 9 (Stretch);
-allowAdjacentIndels until Debian 9 (Stretch);
-cigarUseSeqMatch until Debian 9 (Stretch);
-concordant until Debian 9 (Stretch);
-concordantTemplate until Debian 9 (Stretch);
-fastMaxInterval until Debian 9 (Stretch);
-fastSDP until Debian 9 (Stretch);
-h until Debian 9 (Stretch);
-header until Debian 9 (Stretch);
-hitPolicy until Debian 9 (Stretch);
-ignoreHQRegions until Debian 9 (Stretch);
-ignoreRegions until Debian 9 (Stretch);
-minAlnLength until Debian 9 (Stretch);
-minPctAccuracy until Debian 9 (Stretch);
-noSortRefinedAlignments until Debian 9 (Stretch);
-noSplitSubreads until Debian 9 (Stretch);
-placeRepeatsRandomly until Debian 9 (Stretch);
-printSAMQV until Debian 9 (Stretch);
-randomSeed until Debian 9 (Stretch);
-sam until Debian 9 (Stretch);
-subsample until Debian 9 (Stretch);
-useQuality until Debian 9 (Stretch);
-useccs until Debian 9 (Stretch);
-useccsall until Debian 9 (Stretch);
-useccsdenovo until Debian 9 (Stretch).