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Reconstructs viral consensus sequences from a set of ONT reads.

Project 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 `

  1. 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 `

  1. 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

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