Metadata-Version: 1.2
Name: NGSpeciesID
Version: 0.0.8.1
Summary: Reconstructs viral consensus sequences from a set of ONT reads.
Home-page: https://github.com/ksahlin/NGSpeciesID
Author: Kristoffer Sahlin
Author-email: ksahlin@math.su.se
License: UNKNOWN
Description: NGSpeciesID
        ===========
        
        NGSpeciesID is a tool for clustering and consensus forming of targeted ONT reads. This repository is a modified version of [isONclust](https://github.com/ksahlin/isONclust), where consensus and polishing feautures have been added.
        
        NGSpeciesID is distributed as a python package supported on Linux / OSX with python v3.6. [![Build Status](https://travis-ci.org/ksahlin/NGSpeciesID.svg?branch=master)](https://travis-ci.org/ksahlin/NGSpeciesID).
        
        Table of Contents
        =================
        
          * [INSTALLATION](#INSTALLATION)
            * [Using conda](#Using-conda)
            * [Testing installation](#testing-installation)
          * [USAGE](#USAGE)
            * [Output](#Output)
            * [Parameters](#Parameters)
          * [CREDITS](#CREDITS)
          * [LICENCE](#LICENCE)
        
        
        
        INSTALLATION
        ----------------
        
        
        ### Using conda
        Conda is the preferred way to install NGSpeciesID.
        
        1. Create and activate a new environment called NGSpeciesID
        
        ```
        conda create -n NGSpeciesID python=3.6 pip 
        source activate NGSpeciesID
        ```
        
        2. Install NGSpeciesID 
        
        ```
        pip install NGSpeciesID
        conda install --yes -c bioconda medaka spoa
        ```
        3. You should now have 'NGSpeciesID' installed; try it:
        ```
        NGSpeciesID --help
        ```
        
        Upon start/login to your server/computer you need to activate the conda environment "NGSpeciesID" to run NGSpeciesID as:
        ```
        source activate NGSpeciesID
        ```
        
        4. Install [medaka](https://github.com/nanoporetech/medaka).
        
        
        
        ### Testing installation
        
        **TBD**
        
        
        
        USAGE
        -------
        
        NGSpeciesID needs a fastq file generated by an Oxford Nanopore basecaller.
        
        ```
        NGSpeciesID --ont --consensus --medaka --fastq [reads.fastq] --outfolder [/path/to/output] 
        ```
        The argument `--ont` simply means `--k 13 --w 20`. These arguments can be set manually without the `--ont` flag. Specify number of cores with `--t`. 
        
        
        ### Output
        
        The output consists of clustering and consensus information.
        
        * The final cluster information is given in a tsv file `final_clusters.tsv` present in the specified output folder.
        * Draft spoa consensus sequences of each of the clusters are given as consensus_reference_X.fasta (where X is a number).
        * A folder named “medaka_cl_id_X” is created for each spoa consensus. Each medaka outfolder contains medakas output, including the final polished consensus named (by medaka) as “consensus.fasta”.
        
        
        In the cluster TSV-file, the first column is the cluster ID and the second column is the read accession. For example:
        
        ```
        0 read_X_acc
        0 read_Y_acc
        ...
        n read_Z_acc
        ```
        if there are n reads there will be n rows. Some reads might be singletons. The rows are ordered with respect to the size of the cluster (largest first).
        
        
        
        CREDITS
        ----------------
        
        Please cite [1] when using NGSpeciesID.
        
        1. TBA
        
        
        
        LICENCE
        ----------------
        
        GPL v3.0, see [LICENSE.txt](https://github.com/ksahlin/NGSpeciesID/blob/master/LICENCE.txt).
        
        
        
Keywords: viral sequeces ONT Oxford Nanopore Technologies long reads
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.4
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3.7
Requires-Python: !=3.0.*, !=3.1.*, !=3.2.*, !=3.3.*, <4
