====== AMOS ======

AMOS is a collection of tools and class interfaces for the assembly of DNA reads. 
\\
The package includes a robust infrastructure, modular assembly pipelines, and tools for overlapping, consensus generation, contigging, and assembly manipulation.


  * Install

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apt-get install libqt4-dev

cd /root/
wget http://garr.dl.sourceforge.net/project/amos/amos/3.1.0/amos-3.1.0.tar.gz
tar -xvzf amos-3.1.0.tar.gz
cd amos-3.1.0/

nano -w src/Align/find-tandem.cc

    #include <getopt.h>

./configure --prefix=/usr/local/AMOS
make
make check
make install
ln -s /usr/local/AMOS/bin/* /usr/local/bin/ 
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  * Test

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Minimo -h

 Minimo is a de novo assembler based on the AMOS infrastructure. Minimo uses a
 conservative overlap-layout-consensus algorithm to avoid mis-assemblies and
 can be applied to short reads. The input is a FASTA file and there are options
 to control the stringency of the assembly and the processing of the quality
 scores. By default, the results are in the AMOS format and written to the
 directory where the input FASTA file is located.

 Usage:
     Minimo FASTA_IN [options]

 Options:
     -D QUAL_IN=<file>   Input quality score file (in Phred format)
     -D GOOD_QUAL=<n>    Quality score to set for bases within the clear
                           range if no quality file was given (default: 30)
     -D BAD_QUAL=<n>     Quality score to set for bases outside clear range
                           if no quality file was given (default: 10). If your
                           sequences are trimmed, try the same value as GOOD_QUAL.
     -D MIN_LEN=<n>      Minimum contig overlap length (at least 20 bp,
                           default: 35)
     -D MIN_IDENT=<d>    Minimum contig overlap identity percentage (between 0
                           and 100 %, default: 98)
     -D ALN_WIGGLE=<d>   Alignment wiggle value (from 2 for short reads to 15 for
                           long reads, default: 2)
     -D FASTA_EXP=<n>    Export results in FASTA format (0:no 1:yes, default: 0)
     -D ACE_EXP=<n>      Export results in ACE format (0:no 1:yes, default: 0)
     -D OUT_PREFIX=<s>   Prefix to use for the output file path and name

 Minimo v1.6. Copyright Florent Angly 2010. Under the GPL v3 open-source license.

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