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Copyright (C) 2016 Chan Kuang Lim and CONTRIBUTORS
See LICENSE.txt and CONTRIBUTORS.txt for details.


Description
-----------
Gene Prediction Pipeline for Plant Genomes using Self-Training Gene Models and Transcriptomic Data.


Prerequisites
-------------
In principle, Seqping should run on any POSIX-compliant UNIX system (Linux, Mac OS X, Cygwin), although in practice, it has only been tested on Linux systems.
Native Windows support is not anticipated any time soon.

Seqping is a gene model pipeline. In other words it links together many steps and programs to produce final model. For this reason, you must first install a number of programs that Seqping depends on.
a. BLAST 2.2.25 (ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/)
b. CD-HIT 4.5.4 (http://www.bioinformatics.org/downloads/index.php/cd-hit/)
c. Exonerate 2.2 (http://www.ebi.ac.uk/~guy/exonerate/)
d. GlimmerHMM 3.0 (ftp://ccb.jhu.edu/pub/software/glimmerhmm/)
e. AUGUSTUS 2.6.1 (http://bioinf.uni-greifswald.de/augustus/binaries/)
f. SNAP-2012-05-17 (http://korflab.ucdavis.edu/Software/)
g. MAKER 2.28 (http://www.yandell-lab.org/software/maker.html)
h. EMBOSS 6.4.0 (http://emboss.sourceforge.net/download/)
i. HMMER 3 (http://hmmer.janelia.org/software)
j. RepeatMasker-3-3-0 (http://www.repeatmasker.org/RMDownload.html)
k. NCBI C++ Toolkit (ftp://ftp.ncbi.nih.gov/toolbox/ncbi_tools++/)


Installation
------------
Just download, unzip, and use right there. No compilation step needed.
See INSTALL.txt for details.


Running
-------
Usage: Gene Prediction Pipeline for Plant Genome using Self-Trained Gene Models and Transcriptomic Data
  Arguments:"
    -t  <string>  Transcriptome sequences in FASTA format
    -g  <string>  Genome sequences in FASTA format
    -r  <string>  Reference full length protein sequences in FASTA format
    -f  <string>  Repeat sequences for filtering in FASTA format
    -m  <string>  Repeat data for filtering in HMM format
    -o  <string>  Directory for output
  Options:"
    -e  <string>  BLAST E-value cut-off  [default: 1e-10]
    -p  <int>     Number of processor  [default: 1]
    -l  <string>  Log file [default: model.log]
    -c  <int>     Start the program from which stage [default: 1]
                    1. Prepare Working Directories
                    2. Prepare Training Set
                    3. GlimmerHMM Training
                    4. AUGUSTUS Training
                    5. SNAP Training
                    6. MAKER Prediction
                    7. Filter Procedue
    -q            Enable jobs submit to SGE job scheduler using qsub
    -s            Enable jobs submit to PBS job scheduler using qsub
    -h            Print help message and exit

See RUNNING.txt for details.
Source: README.txt, updated 2016-06-10