Cryptosporidium GP60 Characterization Tool

Tool Functionality and Overview

This tool's intended purpose is to perform Cryptosporidium subtyping utilizing the GP60 genomic target region within the Cryptosporidum genome. The region targets the subtype family, short tandem repeats and secondary repeats within the sequece. The tool works with Sanger sequences and isolate whole genome contig sequences in fasta format.

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Version: Archived (Not maintained)

Organization: NCEZID - Division of Foodborne, Waterborne, and Environmental Diseases (DFWED)

Contact Email: ncezid_shareit@cdc.gov

Description: This tool's intended purpose is to perform Cryptosporidium subtyping utilizing the GP60 genomic target region within the Cryptosporidum genome. The region targets the subtype family, short tandem repeats and secondary repeats within the sequece. The tool works with Sanger sequences and isolate whole genome contig sequences in fasta format.

Exemption: Non-exempt

Keywords: pathogen surveillance, next generation sequencing, bioinformatics, genomics, metagenomics, parasitic disease, Cryptosporidiosis

⚠️ Note: The results produced by this pipeline are not ISO or CLIA-certified and should not be considered diagnostic.

Building Container

To rebuild the container, clone this repository and run the command below: docker build -tag(optional) -file Dockerfile <location>

Requirements:

• Linux Operating system
• Docker
• Perl

Expected Input:

• --fasta Fasta file with 1 or more sanger sequences OR a fasta file containing the assembly of 1 samples
• --blastdb Prebuilt curated blast database
• --data Data type can be sanger or wgs (capitalization does not matter)

Expected Output:

Generates the gp60 subtyping results in a tab delimited text format

Running with Docker

docker run -v $(pwd)/SM_TestData:/test --privileged wdpbcdsphl/crypto_gp60:2.4 perl /scripts/gp60Typer.pl --blastdb db/Crypto_GP60_DB --fasta /test/testInput_SM.fasta --data sanger > results_gp60SM-15.txt

Running with Singularity

singularity exec -B $(pwd)/SM_TestData:/dataIn crypto_gp60-2.4.simg perl /scripts/gp60Typer.pl --blastdb /db/Crypto_GP60_DB --fasta /dataIn/gp60_seqs.fasta --data sanger

Developer

Developed by: Alyssa Kelly, akelley139@gmail.com

Modification by: Shatavia Morrison, SMorrison@cdc.gov

Manuscript prepared by: Anusha Ginni, qxu0@cdc.gov

Clinical Detection Surveillance/WDPB, CDC

Database was updated on: 2021-10-26

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