Amplicon Sequencing Analysis Pipeline (ASAP) for BT-Seq

OVERVIEW:

This is a customized version of the Amplicon Sequencing Analysis Pipeline (ASAP) for the BT-Seq project. ASAP is a highly customizable, automated way to examine amplicon sequencing data. For the full version, see https://github.com/TGenNorth/ASAP.

INSTALLATION:

BT-Seq-ASAP is designed to be run on a compute cluster using a job manager such as SLURM or Torque/PBS. The other dependencies are:

• python 3.x with the following modules: lxml, numpy, pysam, openpyxl, scikit-bio, xmltodict
• bowtie2
• samtools 1.x
• bbmap or trimmomatic

To install, first clone the git repository: git clone [email protected]:TGenNorth/BT-Seq-ASAP.git

Then run, as root: PYTHONPATH=<ASAP_INSTALL_DIRECTORY> easy_install -d <ASAP_INSTALL_DIRECTORY> <SOURCE_REPOSITORY_DIRECTORY>

USAGE:

BT-Seq-ASAP is run in two steps. The first step is analyzing the sequencing data, and the second step is generating reports to see the results.

1) Running the Analysis

analyzeAmplicons -n <RUN_NAME> -j <ASAP_INSTALL_PATH>/assay_data/BT-Seq_all_assays.json -r <DIRECTORY_OF_READ_FILES> -o <OUTPUT_DIRECTORY>

<RUN_NAME> can be whatever you want, the final output file will be: <OUTPUT_DIRECTORY>/<RUN_NAME>_analysis.xml

This final output file is what gets passed into the next command.

For more information about the analyzeAmplicons command, see the full ASAP documentation.

2) Generating Reports

formatOutput -s <ASAP_INSTALL_PATH>/output_transforms/BT-Seq_HeatMap.xsl -x <XML_OUTPUT_FILE> -o <MAIN_OUTPUT_HTML_FILE>

This will generate all the html files for the overview report, which you can open directly in your web browser. Every file will be linked from <MAIN_OUTPUT_HTML_FILE>. <XML_OUTPUT_FILE> is the final output of step 1.

If there are any positives that you want to explore in more depth, you can rerun the formatOutput command with one of the target-specific transforms as the -s argument, and specify a different <MAIN_OUTPUT_HTML_FILE> so it doesn't overwrite the previous one.

<ASAP_INSTALL_PATH>/output_transforms/BT-Seq_Ba_results.xsl for Bacillus antracis results <ASAP_INSTALL_PATH>/output_transforms/BT-Seq_Bp_results.xsl for Burkholderia pseudomallei and mallei results <ASAP_INSTALL_PATH>/output_transforms/BT-Seq_Ft_results.xsl for Francisella tularensis results <ASAP_INSTALL_PATH>/output_transforms/BT-Seq_Yp_results.xsl for Yersinia pestis results

LICENSE:

Copyright © The Translational Genomics Research Institute See the included "LICENSE" document.