Macaw

Macaw is a tool that lineage-types MTB samples and identifies strain mixes in WGS data sets.

Quick-run recipe:

java -jar macaw.jar -o <output.txt> <input.bam>

python macaw-utilities.py interpret -m <output.txt> -o <result>

Downloads and documentation

Versioned production releases: https://github.com/AbeelLab/macaw/releases

Nightly development builds: http://www.abeellab.org/jenkins/macaw/

Source-code: https://github.com/AbeelLab/macaw.git

Submit bugs and features requests: https://github.com/AbeelLab/macaw/issues

Documentation

Running marker detection

Usage: java -jar macaw.jar [options] -o <output> <file>...

Required arguments:

  -o <output> | --output <output>
        File where you want the output to be written
  <file>
        Input files (BAM)

Optional arguments:

  --marker <value>
        File containing marker sequences. This file has to be a multi-fasta file with the headers indicating the name of the markers.
  -t <value> | --threshold <value>
        Threshold to determine absence or presence of a marker (default=5)

Interpreting detected markers

Usage: python macaw-utilities.py interpret -m <marker detection file> -o <output>

Required arguments:

  -m <marker detection file> | --macaw <marker detection file>
        File with absence/presence as determined by macaw.jar
  -o <output> | --output <output>
        Output file prefix (.macaw.interpreted automatically appended)

Condensing results

Usage: python macaw-utilities.py condense -d <input file directory> -o <output>

Required arguments:

  -d <input file directory> | --directory <input file directory>
        Directory with all .interpreted.macaw files in it
  -o <output> | --output <output>
        Output file

Requirements

• Python 2.7 + NumPy + SciPy
• Java 1.7+