Public Repository

Last pushed: 2 years ago
Short Description
Pipeline to map many metagenomes to many reference genomes. Uses bbmap.
Full Description

Data Organization

Need to have all input files together in folder and have one folder called 'metagenomes'(for all the metagenomes you want to map) and one called 'refGenomes'(for all the reference genomes you want to map to)

Running Detached from Container

If you want to save output files which are not coverage.txt, ani.txt, or the sorted bam files, you must run this interactively and copy them to /data before exiting. Otherwise you can run this non interactively.
To run container (not interatively) with default mapping parameters(10 threads, 4g mem each) and retrieve only ani.txt and coverage.txt (see github repo for info about what is in these files) in one command:
docker run -v /home/path2data/folder/:/data -it sstevens/mapall sh -c '/home/'

If you want to change the mapping parameters or retrieve the bam files to add those parameters after above. See usage statement above for more details.

Running Interactively

Starting container from image

To start container interactively and mount data at same time:
docker run -v /home/path2data/folder/:/data -it sstevens/mapall

Running analysis

To run analysis (mapping all v. all and calculating ani and coverage)with default settings(see usage below to change settings) when the container:
home/ Usage

Usage: <threads(default=10)> <Memory limit(default=4g) <minID(default=.8)> <Save .bam files(default=false)>
Example: 3 600m true
Will limit the mapping to only 3 threads at a time and 600 mb per thread and will copy the .bam files to be saved
Order matters, only leave out if keeping subsequent (to the left) arguments blank.
For example if you need the bam files you have to specifiy the memory,the threads and the minID, even if they are default. 10 4g .8 true
But if you only need to change the threads you can leave the other arguments empty. 6

By default the coverage.txt and ani.txt files get moved to the mounted directory (so you will have them when you exit the container).
If you want to include the bam files see the usage statement above. When interactive, you can also copy any files you want to keep into /data and those will also be kept.

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