Trowel - Sequencing Error Corrector Files

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Trowel(v0.1.4.3)
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                                                 by Euncheon Lim in WeigelWorld
  Trowel is a high accurate and massively parallelized error correction module for the Illumina sequencing data. This tool only supports FASTQ file.

  1. Recommanded Environment
     RAM: 64 GB memory
     Cores: 64
     Compiler: Latest GCC

  2. Minimum Environment
     Arch: linux 64bit
     RAM: input file size (IMPORTANT) + hash table size(depending on the genome you used)
     Core(s): 1
     Compiler: GCC 4.3
     Library: Boost 1.53.0

  3. Usage
     (1) vi fastq_files
     (2) save the fastq_files with fastq files.
     (3) trowel -f fastq_files -k 19 -t 32
     Note: k of 19 should be used for A. thaliana-sized genomes. k of 19-23 can be used for H. sapiens-sized genomes (stil 19 is good).  For bacteria genomes, either 15 or 17 is recommended. Do not use k >= 27, such high k reduces the sensitivity of the error corrections.

  4. Contents of fastq_files
     (1) Paired-ended read
         uncorrected_1.fastq uncorrected_2.fastq
     (2) Single-ended read
         uncorrected.fastq
     (3) example fastq_files
         0: a_thal_1.fq a_thal_2.fq
         1: a_thal_single.fq
         2: h_sap_1.fq h_sap_2.fq
         3: d_mel_single.fq
         4: /home/trowel/test_1.fq ./test_2.fq
         (...)

  5. Library Installation
     (0-1) Prerequisite
           sudo apt-get install build-essential python-dev libzip-dev libbz-dev
     (1-1) Download boost 1.53.0
           http://sourceforge.net/projects/boost/files/boost/1.53.0/boost_1_53_0.tar.gz/download
     (1-2) Uncompress and change the directory
           tar xf boost_1_53_0.tar.gz
           cd boost_1_53_0
     (1-3) Install boost
           sudo ./b2 install --prefix=/usr/local

     (2-1) Download Google sparse hash
           http://code.google.com/p/sparsehash/downloads/detail?name=sparsehash-2.0.2.tar.gz&can=2&q=
     (2-2) Uncompress and change the directory
           tar xf sparsehash-2.0.2.tar.gz
           cd sparsehash-2.0.2
     (2-3) Install Google sparsehash
           ./configure --prefix=/usr/local
           sudo make -j8
           sudo make install

  6. Installation
     (1) Download src files
     (2) tar xf trowel.0.1.4.3.src.tar.gz
     (3) cd trowel.0.1.4.3.src
     (4) ./autogen.sh
     (5) sudo cp trowel /usr/bin
     (6) trowel

  7. Licence:
    Trowel: Sequencing Error Corrector for Illumina Short Reads
    Copyright (C) 2013- <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/>.