Download Latest Version megapathDocker.tar.gz (86.5 MB)
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Name Modified Size InfoDownloads / Week
Datasets_availablity 2020-01-21 3.0 kB
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megapathDocker.tar.gz 2020-01-06 86.5 MB
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README 2020-01-06 1.1 kB
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Totals: 3 Items   86.5 MB 0 
MegaPath project

Programming languages: C/C++, bash, perl
Running environment: Linux

The project hass 4 files: megapathDocker.tar.gz, ac-diamond-db.tar.gz, cc-db.tar.gz, megapath-db-20190304.tar.gz. The last 3 files are pre-built databases and available at https://drive.google.com/open?id=1wJVAUmY67UGAFA-HdsT11sTiSgCYJuIJ, https://drive.google.com/open?id=1H42GjIeVjkFcbuhhkNsunxPKGgyKSZ9n, https://drive.google.com/open?id=1E7od9qi3hS4dk3MrY71Pgb7TzlzgM4eo. 

All scripts and source code are in the megapathDocker.tar.gz file. To use MegaPath with Docker, we also provided a 'DockerFile'. Please "docker build" to setup a Docker container. MegaPath takes around 120GB disk space.

The entry script is runMegapath.sh.

Usage: ./runMegaPath.sh -1 <read1.fq> -2 <read2.fq> [options]
    -p  output prefix [megapath]
    -t  number of threads [24]
    -c  NT alignment score cutoff [40]
    -s  SPIKE filter number of stdev [60]
    -o  SPIKE overlap [0.5]
    -L  max read length [150]
    -d  database directory
    -S  skip ribosome filtering
    -H  skip human filtering
    -A  Perform assembly & protein alignment
Source: README, updated 2020-01-06