amr-scripts

Scripts used in the MEG pipelines

amrPipeline.sh

This is the standard pipeline script for the MEG group. It accepts as input paired raw fastq reads and outputs antimicrobial resistance information and optionally microbiome/pathway information. The workflow is as follows:

Run Trimmomatic on the raw fastqs, output to trimmed file directory
Align the trimmed files to the bovine genome using BWA
Filter out reads that align to the bovine genome using SAMTools
Align the remaining reads to the master AMR database
Run SamRatio to get relevant information on the resistome
(Optional) Profile the microbial community with Kraken
(Optional) Profile the microbial community with MetaPhlAn
(Optional) Profile the microbial pathways with HUMAnN2

Two logfiles are kept when running amrPipeline.sh:

logfile.txt (or whatever you name it)
LabNotebook.txt

The logfile is a direct copy of all standard out and standard error from the pipline. The LabNotebook file is a high-level summary of each sample's status as it runs through the pipeline. The LabNotebook file also contains information about the versions of the software used and the paths to the input/output directories when the script was run. It also timestamps each run.

The pipeline has built in file checking and error handling, so if the script exits during a part of the pipeline due to an error, you can simply rerun the script after fixing the error and it won't repeat samples that have already been run. Make sure to delete the output file that threw the error though, since that one will need to be regenerated.

Usage:

amrPipline.sh -i "raw_sequence_reads/*" [options]

Note: you MUST pass the input files in double quotes if you want to use a wildcard to run more than one sample through at a time. The wildcard character must be at the end of the path, so put the fastq files in their own directory with no subdirectories, then pass the wildcard after that directory path, as shown in the above example.

Note: Please pass directory paths with a terminal slash, e.g. /s/bovine/index/projs/canada/analysis/AMR/

Options:

-a | --kraken DIR perform kraken analysis, output to the indicated DIR
-h | --help display the help menu and exit
-i | --input FILES input fastq.gz files (must use quotes with wildcard)
-k | --keep save intermediate files (ex. sam alignment files)
-l | --logfile file name for logfile output, default is logfile.txt
-m | --metaphlan DIR perform metaphlan analysis, output to the indicated DIR
-n | --nonhost DIR directory for nonhost fastq output
-o | --output DIR directory for AMR file output
-t | --threads INT number of threads to use [1]
-tr| --trimmed DIR directory for trimmed file output
-u | --humann2 perform humann2 analysis, output to the indicated DIR

Defaults for options:

--kraken [False]
--input [none]
--keep [False]
--logfile [logfile.txt]
--metaphlan [False]
--nonhost [non_bovine_fastq/]
--output [analysis/AMR/]
--threads [1]
--trimmed [trimmed_fastq_files/]
--humann2 [False]

subsampleFastq.sh

This is a script for subsampling fastqs for rarefaction analysis. This script will do the following:

Call Trimmomatic on the input files
Subsample the files using the dist.py script to given depths

Two logfiles will be kept for this run:

subsample_logfile.txt (or whatever you name it)
LabNotebook.txt