Prerequisites

MERmaid only has three main dependencies:

• Boost C++: Base, MPI and filesystem
• An MPI framework: We only test it with openmpi
• Google sparsehash

Currently, we are only running it on 64-bit Linux. Mac OS X is known to have problems building.

Building

Just run make in the top-level directory.

Running

./mermaid output-file-prefix input-files ..

input-files must be a list of FASTQ files using the Illumina 1.3 quality score format

The outputs will be

• A set of files containing lists of initial k-mers after the initial counting phase. These will be named output-file-prefix.ufx.
• A file containing all the contigs. This will be named output-file-prefix.contigs.0

Mermaid will override default configurations if they are specified in "mermaid.conf". Copy mermaid.conf.example to mermaid.conf and adjust parameter values to override defaults.

TODO

Verify that this README is correct