This docker container performs in silico Legionella spp. identification from Illumina Paired end reads and De novo assemblies. The input file formats are .fastq (for Illumina raw sequencing data) or .fasta/.fa./.fas (for De novo assemblies).
Note: The Mash sketch database file exceed the file size for GitHub. There is a list of all the genomes used to generate the Mash sketch in the /db directory of this repo. The Docker container does contain the entire Mash sketch. Please create an image of the container. If you try to build the container from the source it will fail since the Mash Sketch is not in this repo.
Please use version: SMorrison42/speciesid:0.6
Mash/2.0.0
Perl/5.22.1
Docker:
Illumina Paired End:
docker run -v <your input directory complete path>:/<directory in container> --privileged smorrison42/speciesid:0.6 -fastq1 /<directory in container>/R1.fastq -fastq2 /<directory in container>/R2.fastq > results.txt
Denovo Assemblies:
docker run -v <your input directory complete path>:/<directory in container> --privileged smorrison42/speciesid:0.6 -fasta /<directory in container>/<denovo assembly file> > results.txt
Singularity Pull Container - Do NOT build Mash Sketch file is not in GitHub (exceeded file size limit):
singularity pull docker://smorrison42/speciesid:0.6
Singularity Illumina Paired End:
singularity exec -B <your input directory complete path>:/<directory in container> speciesid-0.6.simg perl /scripts/species_id_tool_agave_3-miseq.pl -fastq1 /<directory in container>/R1.fastq -fastq2 /<directory in container>/R2.fastq > results.txt
The repository utilizes code licensed under the terms of the Apache Software License and therefore is licensed under ASL v2 or later.
This source code in this repository is free: you can redistribute it and/or modify it under the terms of the Apache Software License version 2, or (at your option) any later version.
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Anyone is encouraged to contribute to the repository by forking and submitting a pull request. (If you are new to GitHub, you might start with a basic tutorial.) By contributing to this project, you grant a world-wide, royalty-free, perpetual, irrevocable, non-exclusive, transferable license to all users under the terms of the Apache Software License v2 or later.
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