BAM2fastx tools

The BAM2fastx tools allow conversion of PacBio BAM files into gzipped fasta and fastq files, including demultiplexing of barcoded data.

DEPENDENCIES

Please install Boost and zlib.

INSTALL

• Download source from github

    git clone https://github.com/PacificBiosciences/bam2fastx && cd bam2fastx
  

• Sync your code with the latest git code base:

    git submodule update --init --remote
  

• Create build directory

    mkdir build && cd build
  

• Invoke cmake with Boost and zlib as system libraries

    cmake ..
  

• Or with user-specific paths

    cmake -DBoost_INCLUDE_DIRS=/path/to/boost/include -DZLIB_INCLUDE_DIRS=/path/to/zlib/include -DZLIB_LIBRARIES=/path/to/zlib/lib ..
  

• Build

    make
  

USAGE

Both tools have an identical interface and take BAM and/or DataSet files as input. Examples:

    bam2fasta -o projectName m54008_160330_053509.subreads.bam
    bam2fastq -o myEcoliRuns m54008_160330_053509.subreads.bam m54008_160331_235636.subreads.bam
    bam2fasta -o myHumanGenome m54012_160401_000001.subreadset.xml

HELP

Support is only provided for official and stable SMRT Analysis builds provided by PacBio and not for source builds.