This is the nf-core-based pipeline for SNVPhyl. The SNVPhyl (Single Nucleotide Variant PHYLogenomics) pipeline identifies Single Nucleotide Variants (SNV) within a collection of microbial genomes and constructs a phylogenetic tree from those SNVs. This pipeline is designed to be integrated into IRIDA Next. However, it may be run as a stand-alone pipeline.
Input is provided to SNVPhyl in the form of a samplesheet (passed as --input samplesheet.csv). This samplesheet is a CSV-formated file, which may be provided as a URI (ex: a file path or web address), and has the following format:
| sample | fastq_1 | fastq_2 | reference_assembly |
|---|---|---|---|
| SAMPLE1 | /path/to/sample1_fastq1.fq | /path/to/sample1_fastq2.fq | /path/to/sample1_assembly.fa |
| SAMPLE2 | /path/to/sample2_fastq1.fq |
The columns are defined as follows:
sample: The unique sample identifier to associate with the reads (and optionally the reference assembly).fastq_1: A URI (ex: a file path or web address) to either single-end FASTQ-formatted reads or one pair of pair-end FASTQ-formatted reads.fastq_2: (Optional) Iffastq_1is paired-end, then this field is a URI to reads that are the other pair of reads associated withfastq_1.reference_assembly: (Optional) A URI to a reference assembly associated with the sample, so that it may be referenced on the command line by the sample identifier for use as the reference for the whole pipeline. However, it may be easier to leave these fields blank and specify the reference using the--refgenomeparameter.
The structure of this file is defined in assets/schema_input.json. Please see assets/samplesheet.csv to see an example of a samplesheet for this pipeline.
The mandatory parameters are as follows:
--input: a URI to the samplesheet--output: the directory for pipeline output
Additionally, it is mandatory to have one of either --refgenome or --reference_sample_id (but not both) to specify the reference. Please see the Reference section for more details.
The optional parameters are as follows:
--refgenome: a URI to the reference genome to use during pipeline analysis--reference_sample_id: the sample identifier of a sample in the samplesheet that contains a providedreference_assemblyto use as a reference genome during pipeline analysis
Please use only one of --refgenome or --reference_sample_id and not both.
--window_size: The window size for determining whether a region is high density.--density_threshold: The minimum number of SNVs within the window size for a region to be considered high density.--min_coverage_depth: The minimum depth of coverage for a position within the genome to pass the mapping quality check.--min_mapping_percent_cov: The total percentage of positions within the genome that must have a depth of coverage greater than the minimum depth of coverage specified in order to pass the mapping quality check.--min_mean_mapping_quality: The minimum mean mapping quality score for all reads in a pileup to be included in the analysis.--snv_abundance_ratio: The proportion of reads required to support a variant to be included in the analysis.--min_repeat_length: The minimum length when identifying repeats on the reference genome.--min_repeat_pid: The minimum percent identity when identifying repeats on the reference genome.--skip_density_filter: Whether or not to skip filtering low SNV density regions.
Please refer to the SNVPhyl documentation for more detailed information about pipeline parameters.
-profile: specifies which profiles to use (ex:-profile singularity)-r: specifies which revision to use (ex:-r dev)
In order to run the pipeline with provided data, please run:
nextflow run phac-nml/snvphylnfc -profile singularity --input https://raw.githubusercontent.com/phac-nml/snvphylnfc/dev/assets/samplesheet.csv --refgenome https://raw.githubusercontent.com/phac-nml/snvphylnfc/dev/assets/reference.fasta --outdir results
The pipeline output will be written to a directory named results. A JSON file for integrating data with IRIDA Next will be written to results/iridanext.output.json.gz (please see the Output section for details).
It is also possible to run the pipeline using the test profile as follows:
nextflow run phac-nml/snvphylnfc -profile singularity,test --outdir results
The following output files are generated by the pipeline:
make/snvMatrix.tsv: a pair-wise distance matrix of SNVs that passed all filtering criteriafilter/filterStats.txt: a summary of the number of SNVs filtered within in the SNV Tablephyml/phylogeneticTree.newick: the maximum likelihood phylogeny generated from an alignment of SNVs extracted from the whole genomes of each input filephyml/phylogeneticTreeStats.txt: statistics for the generated phylogenetic treevcf2snv/snvTable.tsv: a table of all detected variant sitesvcf2snv/vcf2core.tsv: a table of the evaluated core positions in each reference fasta sequencevcf2snv/snvAlignment.phy: an alignment of SNVs used to generate the phylogenetic treeverifying/mappingQuality.txt: describes how well the given reads mapped to the reference genome
For more detailed information, please refer to the SNVPhyl Documentation.
A JSON file for loading the data into IRIDA Next is output by this pipeline. The format of this JSON file is specified in our Pipeline Standards for the IRIDA Next JSON. This JSON file is written directly within the --outdir provided to the pipeline with the name iridanext.output.json.gz (ex: [outdir]/iridanext.output.json.gz).
{
"files": {
"global": [
{
"path": "make/snvMatrix.tsv"
},
{
"path": "filter/filterStats.txt"
},
{
"path": "phyml/phylogeneticTreeStats.txt"
},
{
"path": "phyml/phylogeneticTree.newick"
},
{
"path": "vcf2snv/snvTable.tsv"
},
{
"path": "vcf2snv/vcf2core.tsv"
},
{
"path": "vcf2snv/snvAlignment.phy"
},
{
"path": "verifying/mappingQuality.txt"
}
],
"samples": {
}
},
"metadata": {
"samples": {
}
}
}
Within the files section of this JSON file, all of the output paths are relative to the --outdir results. Therefore, "path": "phyml/phylogeneticTree.newick" refers to a file located within results/phyml/phylogeneticTree.newick.
This pipeline uses code and infrastructure developed and maintained by the nf-core community, reused here under the MIT license.
The nf-core framework for community-curated bioinformatics pipelines.
Philip Ewels, Alexander Peltzer, Sven Fillinger, Harshil Patel, Johannes Alneberg, Andreas Wilm, Maxime Ulysse Garcia, Paolo Di Tommaso & Sven Nahnsen.
Nat Biotechnol. 2020 Feb 13. doi: 10.1038/s41587-020-0439-x. In addition, references of tools and data used in this pipeline are as follows:
Copyright 2023 Government of Canada
Licensed under the MIT License (the "License"); you may not use this work except in compliance with the License. You may obtain a copy of the License at:
https://opensource.org/license/mit/
Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.
This pipeline includes source code from a nf-core pipeline for SNVPhyl developed by Jill Hagey as a work of the United States Government that was not subject to domestic copyright protection under 17 USC § 105. This work by the United States Government is in the public domain within the United States, and copyright and related rights for the work worldwide are waived through the CC0 1.0 Universal public domain dedication.
The included source code developed by Jill Hagey as a work of the United States Government was distributed under the Apache Software License version 2. A copy of the Apache Software License is included in this repository.
Any such source files in this project that are included from or derived from the original work by Jill Hagey will include a notice.