Reconstructs viral consensus sequences from a set of ONT reads.
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)
### Using conda Conda is the preferred way to install NGSpeciesID.
- Create and activate a new environment called NGSpeciesID
` conda create -n NGSpeciesID python=3.6 pip source activate NGSpeciesID `
- Install NGSpeciesID
` pip install NGSpeciesID conda install --yes -c conda-forge -c bioconda medaka openblas==0.3.3 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 `
- Install [medaka](https://github.com/nanoporetech/medaka).
### Testing installation
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.
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).
Please cite  when using NGSpeciesID.
GPL v3.0, see [LICENSE.txt](https://github.com/ksahlin/NGSpeciesID/blob/master/LICENCE.txt).
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