snpiphy is a workflow pipeline for the automated generation of SNP derived phylogenetic trees. This pipeline quickly generates a SNP-derived tree using a single reference sequence and established tools. Users need to provide a high-quality reference sequence and a directory containing single-end (with the -s option) or interleaved fastq. Reads can be provided as uncompressed .fastq or gzip-compressed .fastq.gz. Currently, split file paired reads or reads from multiple runs are not supported. Assemblies in fasta format can also be provided but fastq reads are preferred.
snpiphy requires a linux-based operating system and the following:
- python (>=3.5)
- biopython (>=1.72)
- pandas (>=0.23.4)
- numpy (>=1.16.0)
- snippy (>=4.3.6)
- gubbins (>=2.3.4)
To download and install snpiphy with all dependencies use conda:
conda install -c conda-forge -c bioconda snpiphy
or pip (requires manual dependency installation):
pip install git+https://github.com/bogemad/snpiphy.git
or a manual install (again this requires you to manually install dependencies):
git clone https://github.com/bogemad/snpiphy.git
cd snpiphy
python setup.py install
usage: snpiphy [-h] -o OUTDIR -r REFERENCE [-q READS_DIR] [-l READS_LIST]
[-c CUTOFF] [-p PREFIX] [-t THREADS] [-j] [-s] [-m]
[-b {raxml,fasttree}] [-f] [-n] [--version] [-v]
snpiphy - An automated snp phylogeny pipeline.
required arguments:
-o OUTDIR, --output-directory OUTDIR
Path to the output directory. A directory will be
created if one does not exist.
-r REFERENCE, --reference REFERENCE
Path to the reference sequence. Only fasta format is
accepted currently.
input arguments - required, provide only one:
-q READS_DIR, --input_dir READS_DIR
Path to a directory with your interleaved fastq
sequencing reads, single-end sequencing reads (use
with the -s option) or fasta assemblies.
-l READS_LIST, --input_list READS_LIST
Path to a tab-separated file containing read paths and
paired status. Best used when running a combination of
single-end and paired-end data or if your data is
spread across multiple directories. Run
'snpiphy_generate_input_list' to generate an example
list.
optional arguments:
-h, --help show this help message and exit
-c CUTOFF, --cov_cutoff CUTOFF
Percent coverage of reference sequence (0-100%) used
to reject a sample. Samples lower than this threshold
will be excluded from phylogenetic pipeline steps.
Defaults to 85%.
-p PREFIX, --prefix PREFIX
Prefix for output files
-t THREADS, --threads THREADS
Number of threads to use for multiprocessing.
-j, --parallel Use GNU parallel to run multiple instances of snippy
(can speed things up if you have multiple cores
available)
-s, --single_end fastq reads are single end instead of paired-end. Use
for ion torrent or non-paired end illumina data
-m, --gamma_model Use GTRGAMMA model instead of GTRCAT during the
gubbins and RAxML tree building steps.
-b {raxml,fasttree}, --tree_builder {raxml,fasttree}
Algorithm used for building the phylogenetic tree
(default: raxml)
-f, --force Overwrite files in the output directories.
-n, --no_recombination_filter
Don't filter potential recombination events. Use for
organisms that are known undergo low amounts of
recombination.
--version show program's version number and exit
-v, --verbose Increase verbosity on command line output (n.b.
verbose output is always saved to snpiphy.log in the
output directory).