Crosscut: Multiple genome representation Files

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Poseidon(v1.0.2)
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                                                 by Euncheon Lim in WeigelWorld


  Due to the conflict of interests, the source codes are unavailable until the publication
  of the algorithm finished. Only the binaries are provided.

  Poseidon is a highly senstive and efficient taxonomy classifier based on a population index,
  which combines an FM-index and a higher-level layer describing the texts in a dataset. For
  a taxonomy classifier, taxonomy information are used to describe the texts. The algorithm has
  been developed since 6. Feb. 2015. The algorithm is presented in the CSHL conference (Genome
  Informatics) on 30, Oct, 2015.

  I especially thank Prof. Weigel for his care and supports during my PhD study.
  I am inspired by the aim of MEGAN software written by my co-supervisor, Prof. Huson.
  I also appreciate Dr. Jared Simpson for explaining modules in SGA.
  Alex Bowe nicely illustrated the backward searches on an FM-index.

  The burrows wheeler transformed text is currently generated by ropebwt2, which
  is written by Heng Li. The basic string operations are performed by modified modules taken from
  SGA package written by Dr. Simpson. They are modified to support for searching ambiguous bases.

  The taxonomy information are rendered by taxonomy tree and taxonomy map.
  This tool supports for single-end FASTA and FASTQ files and is enabled with parallel IO.

  1. Recommanded Environment
     RAM: 64 GB memory
     Cores: 64
     Compiler: Latest GCC
     Location of FASTQ: SSDs or RAID enabled with parallel access

  2. Minimum Environment
     Arch: linux 64bit
     RAM: 16 GB memory
     Core(s): 1

  3. Usage
     (1) Create a list file containing paths for UNCOMPRESSED FASTA or FASTQ files.
         each line indicates a file to be classified
           ebola_virus_infected_individual.fa
           Corona_virus_infected_human.fq
           Corona_virus_infected_bovine.fq
           ...
     (2) poseidon -f file_list -r inc -e exc
     Note: -r parameter indicates a folder containing genomes of known bacteria or viruses or fungi
           -e parameter indicates a folder containing background genomes such as H. sapiens or A. Thaliana

  4. Library Installation
     (0-1) Prerequisite (especially, zlib should be installed)
           sudo apt-get install build-essential python-dev libzip-dev libbz-dev zlib1g-dev libsparsehash-dev
     (1-1) Download boost 1.55.0
           wget http://sourceforge.net/projects/boost/files/boost/1.55.0/boost_1_55_0.tar.gz/download
           mv download boost_1_55_0.tar.gz
     (1-2) Uncompress and change the directory
           tar xf boost_1_55_0.tar.gz
           cd boost_1_55_0
     (1-3) Install boost
           ./bootstrap.sh
           sudo ./b2 install --prefix=/usr/local
     (1-4) export the boost lib path to "LIBRARY_PATH" environment variable in .bashrc
           export LIBRARY_PATH=$LIBRARY_PATH:/usr/local/lib

  5. Installation
     (0) Download compressed binary file
     (1) ./toy_example.sh

  6. Licence:
    Poseidon: A highly sensitive and efficient taxonomy classifier
    Copyright (C) 2015- <Euncheon Lim>

    This program is free software: you can redistribute it and/or modify
    it under the terms of the GNU General Public License as published by
    the Free Software Foundation, either version 3 of the License, or
    (at your option) any later version.

    This program is distributed in the hope that it will be useful,
    but WITHOUT ANY WARRANTY; without even the implied warranty of
    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
    GNU General Public License for more details.

    You should have received a copy of the GNU General Public License
    along with this program.  If not, see <http://www.gnu.org/licenses/>.