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Profiler for metagenomics based on NGLess
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luispedro ENH Add taxonomic profiling
For human, use motus + specI; for others, use only specIs (as motus is
only for the human gut).
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ChangeLog ENH Add taxonomic profiling Jul 13, 2018
README.md
dog-gut-profiler.ngl
human-gut-profiler.ngl ENH Add taxonomic profiling Jul 13, 2018
marine-profiler.ngl ENH Update to use ngless 0.9 Jul 11, 2018
mouse-gut-profiler.ngl
pig-gut-profiler.ngl

README.md

NGLESS-PROFILER

http://ngless.embl.de

This is a collection of predefined ngless pipelines for processing shotgun metagenomes.

  1. human-gut.ngl for human gut samples

  2. marine.ngl for marine samples

  3. mouse-gut.ngl for mouse gut samples

  4. dog-gut.ngl for dog gut samples

  5. pig-gut.ngl for pig gut samples

These are predefined, but users are encouraged to adapt them to their specific needs.

INSTALL

You need to

  1. install ngless. The recommended way is through bioconda:

    conda install -c bioconda ngless

Alternatively, see the ngless documentation on how to install it.

  1. copy the profiling scripts to next to where your data lives

USAGE

To use the profiler, select the appropriate script (e.g., human-gut.ngl for human gut samples), put all the FastQ files from the same sample in the same directory (INPUT-DIRECTORY) with the extension .fq.gz or fastq.gz and run:

ngless human-gut.ngl INPUT-DIRECTORY OUTPUT-DIRECTORY

You can use all the ngless command line options to set options. For example, to use 8 cores, use:

ngless --threads=8 human-gut.ngl INPUT-DIRECTORY OUTPUT-DIRECTORY

If you want very verbose output:

ngless --threads=8 --trace human-gut.ngl INPUT-DIRECTORY OUTPUT-DIRECTORY

GETTING HELP

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