Metadata-Version: 1.2
Name: sequana-denovo
Version: 0.8.0
Summary: Denovo Assembly from FASTQ files
Home-page: https://github.com/sequana/
Author: thomas cokelaer
Author-email: thomas.cokelaer@pasteur.fr
Maintainer: thomas cokelaer
Maintainer-email: thomas.cokelaer@pasteur.fr
License: new BSD
Description: This is is the **denovo** pipeline from the `Sequana <https://sequana.readthedocs.org>`_ projet
        
        :Overview: a de-novo assembly pipeline for short-read sequencing data
        :Input: A set of FastQ files
        :Output: Fasta, VCF, HTML report
        :Status: production
        :Citation: Cokelaer et al, (2017), ‘Sequana’: a Set of Snakemake NGS pipelines, Journal of Open Source Software, 2(16), 352, JOSS DOI doi:10.21105/joss.00352
        
        
        Installation
        ~~~~~~~~~~~~
        
        You must install Sequana first::
        
            pip install sequana
        
        Then, just install this package::
        
            pip install sequana_denovo
        
        
        Usage
        ~~~~~
        
        ::
        
            sequana_pipelines_denovo --help
            sequana_pipelines_denovo --input-directory DATAPATH 
        
        This creates a directory with the pipeline and configuration file. You will then need 
        to execute the pipeline::
        
            cd denovo
            sh denovo.sh  # for a local run
        
        This launch a snakemake pipeline. If you are familiar with snakemake, you can 
        retrieve the pipeline itself and its configuration files and then execute the pipeline yourself with specific parameters::
        
            snakemake -s denovo.rules -c config.yaml --cores 4 --stats stats.txt
        
        Or use `sequanix <https://sequana.readthedocs.io/en/master/sequanix.html>`_ interface.
        
        Requirements
        ~~~~~~~~~~~~
        
        This pipelines requires the following executable(s):
        
        - spades
        - busco
        - bwa
        - khmer : there is not executable called kmher but a set of executables (.e.g .normalize-by-median.py)
        - freebayes
        - picard
        - prokka
        - quast
        - spades
        - sambamba
        - samtools
        
        
        
        .. image:: https://raw.githubusercontent.com/sequana/sequana_denovo/master/sequana_pipelines/denovo/dag.png
        
        
        Details
        ~~~~~~~~~
        
        
        Snakemake *de-novo* assembly pipeline dedicates to small genome like bacteria.
        It is based on `SPAdes <http://cab.spbu.ru/software/spades/>`_.
        The assembler corrects reads and then assemble them using different size of kmer.
        If the correct option is set, SPAdes corrects mismatches and short INDELs in
        the contigs using BWA.
        
        The sequencing depth can be normalised with `khmer <https://github.com/dib-lab/khmer>`_.
        Digital normalisation converts the existing high coverage regions into a Gaussian
        distributions centered around a lower sequencing depth. To put it another way,
        genome regions covered at 200x will be covered at 20x after normalisation. Thus,
        some reads from high coverage regions are discarded to reduce the quantity of data.
        Although the coverage is drastically reduce, the assembly will be as good or better
        than assembling the unnormalised data. Furthermore, SPAdes with normalised data
        is notably speeder and cost less memory than without digital normalisation.
        Above all, khmer does this in fixed, low memory and without any reference
        sequence needed.
        
        The pipeline assess the assembly with several tools and approach. The first one
        is `Quast <http://quast.sourceforge.net/>`_, a tools for genome assemblies
        evaluation and comparison. It provides a HTML report with useful metrics like
        N50, number of mismatch and so on. Furthermore, it creates a viewer of contigs
        called `Icarus <http://quast.sourceforge.net/icarus.html>`_.
        
        The second approach is to characterise coverage with sequana coverage and
        to detect mismatchs and short INDELs with
        `Freebayes <https://github.com/ekg/freebayes>`_.
        
        The last approach but not the least is `BUSCO <http://busco.ezlab.org/>`_, that
        provides quantitative measures for the assessment of genome assembly based on
        expectations of gene content from near-universal single-copy orthologs selected
        from `OrthoDB <http://www.orthodb.org/>`_.
        
Keywords: snakemake, ngs, denovo, assembly, short read
Platform: Linux
Platform: Unix
Platform: MacOsX
Platform: Windows
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Education
Classifier: Intended Audience :: End Users/Desktop
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: BSD License
Classifier: Operating System :: OS Independent
Classifier: Programming Language :: Python :: 3.5
Classifier: Programming Language :: Python :: 3.6
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Topic :: Scientific/Engineering :: Information Analysis
Classifier: Topic :: Scientific/Engineering :: Mathematics
Classifier: Topic :: Scientific/Engineering :: Physics
