Metadata-Version: 2.1
Name: referenceseeker
Version: 1.4
Summary: ReferenceSeeker: rapid determination of appropriate reference genomes.
Home-page: https://github.com/oschwengers/referenceseeker
Author: Oliver Schwengers
Author-email: oliver.schwengers@computational.bio.uni-giessen.de
License: GPLv3
Project-URL: Source, https://github.com/oschwengers/referenceseeker
Project-URL: Bug Reports, https://github.com/oschwengers/referenceseeker/issues
Description: [![License: GPL v3](https://img.shields.io/badge/License-GPL%20v3-brightgreen.svg)](https://github.com/oschwengers/referenceseeker/blob/master/LICENSE)
        ![PyPI - Python Version](https://img.shields.io/pypi/pyversions/referenceseeker.svg)
        ![GitHub release](https://img.shields.io/github/release/oschwengers/referenceseeker.svg)
        ![PyPI](https://img.shields.io/pypi/v/referenceseeker.svg)
        ![PyPI - Status](https://img.shields.io/pypi/status/referenceseeker.svg)
        ![Conda](https://img.shields.io/conda/v/bioconda/referenceseeker.svg)
        ![Conda](https://img.shields.io/conda/pn/bioconda/referenceseeker.svg)
        
        # ReferenceSeeker: rapid determination of appropriate reference genomes.
        
        ## Contents
        - [Description](#description)
        - [Input & Output](#input-output)
        - [Installation](#installation)
        - [Usage](#usage)
        - [Examples](#examples)
        - [Databases](#databases)
        - [Dependencies](#dependencies)
        - [Citation](#citation)
        
        ## Description
        ReferenceSeeker determines closely related reference genomes from
        RefSeq (<https://www.ncbi.nlm.nih.gov/refseq>) following a scalable hierarchical
        approach combining an ultra-fast kmer profile-based database lookup of candidate
        reference genomes and subsequent computation of specific average nucleotide
        identity (ANI) values for the rapid determination of suitable reference genomes.
        
        ReferenceSeeker computes kmer-based genome distances between a query genome and
        and a database built on RefSeq genomes via Mash (Ondov et al. 2016). Therefore,
        only complete genomes or those stated as 'representative' or 'reference' genome
        are included. ReferenceSeeker offers pre-built databases for a broad spectrum of
        microbial taxonomic groups, i.e. bacteria, archaea, fungi, protozoa and viruses.
        For resulting candidates ReferenceSeeker subsequently computes ANI values picking
        genomes meeting community standard thresholds by default (ANI >= 95 % & conserved DNA >= 69 %)
        (Goris, Konstantinos et al. 2007) ranked by the product of ANI and conserved DNA values.
        
        The reasoning for subsequent calculations of both ANI and conserved DNA values
        is that Mash distance values correlate well with ANI values for closely
        related genomes but the same is not true for conserved DNA values. A kmer
        fingerprint-based comparison alone cannot distinguish if a kmer is missing
        due to a SNP, for instance or a lack of the kmer-comprising subsequence.
        As DNA conservancy (next to DNA identity) is very important for many kinds of
        analyses, e.g. reference based SNP detections, ranking potential reference
        genomes based on a mash distance alone is often not sufficient in order to select
        the most appropriate reference genomes. If desired, ANI and conserved DNA values
        can be computed bidirectionally.
        
        ![Mash D vs. ANI / conDNA](mash-ani-cdna.mini.png?raw=true)
        
        ## Input & Output
        ### Input:
        Path to a taxon database and a draft or finished genome in fasta format:
        ```
        $ referenceseeker ~/bacteria GCF_000013425.1.fna
        ```
        
        ### Output:
        Tab separated lines to STDOUT comprising the following columns:
        
        Unidirectionally (query -> references):
        - RefSeq Assembly ID
        - Mash Distance
        - ANI
        - Conserved DNA
        - NCBI Taxonomy ID
        - Assembly Status
        - Organism
        
        ```
        #ID	Mash Distance	ANI	Con. DNA	Taxonomy ID	Assembly Status	Organism
        GCF_000013425.1	0.00000	100.00	100.00	93061	complete	Staphylococcus aureus subsp. aureus NCTC 8325
        GCF_001900185.1	0.00002	100.00	99.89	46170	complete	Staphylococcus aureus subsp. aureus HG001
        GCF_900475245.1	0.00004	100.00	99.57	93061	complete	Staphylococcus aureus subsp. aureus NCTC 8325 NCTC8325
        GCF_001018725.2	0.00016	100.00	99.28	1280	complete	Staphylococcus aureus FDAARGOS_10
        GCF_003595465.1	0.00185	99.86	96.81	1280	complete	Staphylococcus aureus USA300-SUR6
        GCF_003595385.1	0.00180	99.87	96.80	1280	complete	Staphylococcus aureus USA300-SUR2
        GCF_003595365.1	0.00180	99.87	96.80	1280	complete	Staphylococcus aureus USA300-SUR1
        GCF_001956815.1	0.00180	99.87	96.80	46170	complete	Staphylococcus aureus subsp. aureus USA300_SUR1
        ...
        ```
        Bidirectionally (query -> references [QR] & references -> query [RQ]):
        - RefSeq Assembly ID
        - Mash Distance
        - QR ANI
        - QR Conserved DNA
        - RQ ANI
        - RQ Conserved DNA
        - NCBI Taxonomy ID
        - Assembly Status
        - Organism
        
        ```
        #ID	Mash Distance	QR ANI	QR Con. DNA	RQ ANI	RQ Con. DNA	Taxonomy ID	Assembly Status	Organism
        GCF_000013425.1	0.00000	100.00	100.00	100.00	100.00	93061	complete	Staphylococcus aureus subsp. aureus NCTC 8325
        GCF_001900185.1	0.00002	100.00	99.89	100.00	99.89	46170	complete	Staphylococcus aureus subsp. aureus HG001
        GCF_900475245.1	0.00004	100.00	99.57	99.99	99.67	93061	complete	Staphylococcus aureus subsp. aureus NCTC 8325 NCTC8325
        GCF_001018725.2	0.00016	100.00	99.28	99.95	98.88	1280	complete	Staphylococcus aureus FDAARGOS_10
        GCF_001018915.2	0.00056	99.99	96.35	99.98	99.55	1280	complete	Staphylococcus aureus NRS133
        GCF_001019415.2	0.00081	99.99	94.47	99.98	99.36	1280	complete	Staphylococcus aureus NRS146
        GCF_001018735.2	0.00096	100.00	94.76	99.98	98.58	1280	complete	Staphylococcus aureus NRS137
        GCF_003354885.1	0.00103	99.93	96.63	99.93	96.66	1280	complete	Staphylococcus aureus 164
        ...
        ```
        
        ## Installation
        Platon can be installed via Conda and Git(Hub).
        
        In either case, a taxon database must be downloaded which we provide for download at Zenodo:
        [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3562005.svg)](https://doi.org/10.5281/zenodo.3562005)
        For more information scroll to [Databases](#databases).
        
        ### Conda / BioConda
        The preferred way to install and run ReferenceSeeker is [Conda](https://conda.io/docs/install/quick.html) using the [Bioconda](https://bioconda.github.io/) channel:
        ```
        $ conda install -c conda-forge -c bioconda -c defaults referenceseeker
        $ referenceseeker --help
        ```
        
        ### GitHub
        Alternatively, you can use this raw GitHub repository:
        1. install necessary Python dependencies (if necessary)
        2. clone the latest version of the repository
        3. download and extract a databases
        
        Example:
        ```
        $ pip3 install --user biopython
        $ git clone https://github.com/oschwengers/referenceseeker.git
        $ ./referenceseeker/bin/referenceseeker --help
        ```
        
        ## Usage
        Usage:
        ```
        usage: referenceseeker [-h] [--crg CRG] [--ani ANI]
                               [--conserved-dna CONSERVED_DNA] [--unfiltered]
                               [--bidirectional] [--verbose] [--threads THREADS]
                               [--version]
                               <database> <genome>
        
        Rapid determination of appropriate reference genomes.
        
        positional arguments:
          <database>            ReferenceSeeker database path
          <genome>              target draft genome in fasta format
        
        optional arguments:
          -h, --help            show this help message and exit
          --crg CRG, -r CRG     max number of candidate reference genomes to pass kmer
                                prefilter (default = 100)
          --ani ANI, -a ANI     ANI threshold value (default = 0.95)
          --conserved-dna CONSERVED_DNA, -c CONSERVED_DNA
                                Conserved DNA threshold value (default = 0.69)
          --unfiltered, -u      set kmer prefilter to extremely conservative values
                                and skip species level ANI cutoffs (ANI >= 0.95 and
                                conserved DNA >= 0.69
          --bidirectional, -b   Compute bidirectional ANI values (default = False)
          --verbose, -v         print verbose information
          --threads THREADS, -t THREADS
                                number of threads to use (default = number of
                                available CPUs)
          --version, -V         show program's version number and exit
        ```
        
        ## Examples
        Simple:
        ```
        $ # referenceseeker <REFERENCE_SEEKER_DB> <GENOME>
        $ referenceseeker bacteria/ genome.fasta
        ```
        
        Expert: verbose output and increased output of candidate reference genomes using a defined number of threads:
        ```
        $ # referenceseeker --crg 500 --verbose --threads 8 <REFERENCE_SEEKER_DB> <GENOME>
        $ referenceseeker --crg 500 --verbose --threads 8 bacteria/ genome.fasta
        ```
        
        ## Databases
        ReferenceSeeker depends on custom databases based on reference, representative as
        well as complete NCBI RefSeq genomes comprising kmer hash profiles and taxonomic information.
        We provide the following pre-built databases based on RefSeq 2019-07-02 via [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.3562005.svg)](https://doi.org/10.5281/zenodo.3562005) :
        
        | Taxon | URL | # Genomes | Size Zipped | Size Unzipped |
        | :---: | --- | ---: | :---: | :---: |
        | bacteria | <https://zenodo.org/record/3562005/files/bacteria.tar.gz?download=1> | 18,229 | 22 Gb | 71 Gb |
        | archaea | <https://zenodo.org/record/3562005/files/archaea.tar.gz?download=1> | 417 | 364 Mb | 1.2 Gb |
        | fungi | <https://zenodo.org/record/3562005/files/fungi.tar.gz?download=1> | 288 | 2.6 Gb | 8 Gb |
        | protozoa | <https://zenodo.org/record/3562005/files/protozoa.tar.gz?download=1> | 88 | 1 Gb | 3.4 Gb |
        | viral | <https://zenodo.org/record/3562005/files/viral.tar.gz?download=1> | 9,264 | 608 Mb | 835 Mb |
        
        Updated database versions reflecting the latest RefSeq versions can be built
        with a shell script and nextflow pipeline.
        
        Download and install Nextflow:
        ```
        $ curl -fsSL get.nextflow.io | bash
        ```
        
        Build database:
        ```
        $ export REFERENCE_SEEKER_HOME=<REFERENCE_SEEKER_DIR>
        $ sh $REFERENCE_SEEKER_HOME/build-db.sh <DB_TYPE_OPTION>
        ```
        
        List of available database options:
        ```
        $ sh build-db.sh
        	-b (bacteria)
        	-a (archaea)
        	-v (viral)
        	-f (fungi)
        	-p (protozoa)
        ```
        
        ## Dependencies
        ReferenceSeeker needs the following dependencies:
        - Python (3.5.2), Biopython (1.71)
        - Mash (2.2) <https://github.com/marbl/Mash>
        - MUMmer (4.0.0-beta2) <https://github.com/gmarcais/mummer>
        
        ReferenceSeeker has been tested against aforementioned versions.
        
        ## Citation
        
        > ReferenceSeeker: rapid determination of appropriate reference genomes. Oliver Schwengers, Torsten Hain, Trinad Chakraborty, Alexander Goesmann. bioRxiv 863621; doi: https://doi.org/10.1101/863621
        
Keywords: bioinformatics,ngs,wgs,microbial genomics
Platform: UNKNOWN
Classifier: Operating System :: POSIX :: Linux
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Development Status :: 5 - Production/Stable
Classifier: License :: OSI Approved :: GNU General Public License v3 (GPLv3)
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Environment :: Console
Classifier: Intended Audience :: Science/Research
Classifier: Natural Language :: English
Requires-Python: >=3.5
Description-Content-Type: text/markdown
