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BLASR: The PacBio® long read aligner
C++ C Perl Other
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alignment Add blasr back to exes to build
assembly Initial import of //depot/software/assembly/cpp/ from the state at re…
bwtutils Initial import of //depot/software/assembly/cpp/ from the state at re…
cdna Initial import of //depot/software/assembly/cpp/ from the state at re…
common Fix a bug which causes loadPulses compiled with gcc4.8 to fail.
ctest Prop change (140573) to legacy blasr.
gffutils Initial import of //depot/software/assembly/cpp/ from the state at re…
gold_standard bug 25021 - remove one warning from the cpp Makefiles
jabon bug 25021 - remove one warning from the cpp Makefiles
pbihdfutils bug 25021 - remove one warning from the cpp Makefiles
pelusa bug 25021 - remove one warning from the cpp Makefiles
samutils bug 25021 - remove one warning from the cpp Makefiles
sequtils Fix Makefile for bsdb: hdf5 lib is required to compile bsdb
simulator Update simulator alchemy and StoreQualityByContextFromCmpH5.
studies Initial import of //depot/software/assembly/cpp/ from the state at re…
testing Initial import of //depot/software/assembly/cpp/ from the state at re…
utest Migrate blasr unit test datasets to /mnt/secondary-siv/testdata
utils Initial import of //depot/software/assembly/cpp/ from the state at re…
BinifyMakedep.pl Initial import of //depot/software/assembly/cpp/ from the state at re…
LICENSE.txt Initial import of //depot/software/assembly/cpp/ from the state at re…
Makefile Remove "||true" from Makefile, so that an error code will be returned
MoveODependenciesToBin.pl Initial import of //depot/software/assembly/cpp/ from the state at re…
README.md Update README.md
README.txt bug 18909
common.mk bug 25263 - keep using -static in the build
make.rules bug 25021 - remove one warning from the cpp Makefiles

README.md

NEWS: Try the refactored blasr code base

We have refactored the blasr code base and will replace this blasr repo with the refactored one soon.

Please try it now if you are interested, and report any issue to yli@pacificbiosciences.com.

  • > git clone git@github.com:ylipacbio/refactored_blasr_II.git --recursive

Installation

1. Requirements

To build BLASR, you must have hdf 1.8.0 or above installed and configured with c++ support (you should have the library libhdf5_cpp.a). If you are intalling the entire PacBio secondary analysis software suite, appropriate hdf libraries are already distributed and no configuration is necessary. Otherwise, it is necessary to point two environment variables, HDF5INCLUDEDIR and HDF5LIBDIR to the locations of the HDF5 libraries.

For example:

  • > export HDF5INCLUDEDIR=/usr/include/hdf
  • > export HDF5LIBDIR=/usr/lib/hdf

2. Build the source tree

  • > make

3. The executable will be in alignment/bin/blasr

  • > cd alignment/bin/blasr

Running BLASR

Typing blasr -h or blasr -help on the command line will give you a list of options. At the least, provide a fasta, fastq, or bas.h5 file, and a genome.

Some typical use cases:

  • Align reads from reads.bas.h5 to ecoli_K12 genome, and output in SAM format.

    • > blasr reads.bas.h5 ecoli_K12.fasta -sam
  • Same as above, but with soft clipping

    • > blasr reads.bas.h5 ecoli_K12.fasta -sam -clipping soft
  • Use multiple threads

    • > blasr reads.bas.h5 ecoli_K12.fasta -sam -clipping soft -out alignments.sam -nproc 16
  • Include a larger minimal match, for faster but less sensitive alignments

    • > blasr reads.bas.h5 ecoli_K12.fasta -sam -clipping soft -minMatch 15
  • Produce alignments in a pairwise human readable format

    • > blasr reads.bas.h5 ecoli_K12.fasta -m 0
  • Use a precomputed suffix array for faster startup

    • > sawriter hg19.fasta.sa hg19.fasta #First precompute the suffix array
    • > blasr reads.bas.h5 hg19.fasta -sa hg19.fasta.sa
  • Use a precomputed BWT-FM index for smaller runtime memory footprint, but slower alignments.

    • > sa2bwt hg19.fasta hg19.fasta.sa hg19.fasta.bwt
    • > blasr reads.bas.h5 hg19.fasta -bwt hg19.fasta.bwt

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