NAME

       run_mapsembler2_pipeline - pipelines the mapsembler2 tools

SYNOPSIS

       run_mapsembler_and_phaser.sh -s <starter.fasta> -r <reads.faste> -t [1/2/3/4]<options>

DESCRIPTION

       run_mapsembler_pipeline.sh, a pipelining mapsembler2_extremities, mapsembler2_extend and kissread_g

OPTIONS

       -s: file containing starters (fasta)

       -r  list of reads separated by space, surrounded by the '"' character. Note that reads may be in fasta or
              fastq    format,    gzipped    or    not.    Example:    -r     "data_sample/reads_sequence1.fasta
              data_sample/reads_sequence2.fasta.gz".

       -t: kind of assembly: 1=unitig (fasta), 2=contig (fasta), 3=unitig (graph), 4=contig(graph)

   OPTIONAL
       -p prefix. All out files will start with this prefix. Example: -p my_prefix

       -k value. Set the length of used kmers. Must fit the compiled value. Default=31. Example -k 31

       -c value. Set the minimal coverage. Default=5. Example -c 5

       -d  value.  Set the number of authorized substitutions used while mapping reads on found SNPs. Default=1.
              Example: -d 1

       -g value. Estimated genome size. Used only to control memory usage. e.g. 3 billion (3000000000) uses  4Gb
              of RAM. Default=10 million. Example: -d 10000000

       -f value. Set the process of search in the graph (1=Breadth  and 2=Depth). Default=1. Example: -f 1

       -x value. Set the maximal nodes length . Default=40. Example: -x 40

       -y value. Set the maximal graph depth . Default=10000. Example: -y 10000

       -h Prints this message and exist

SEE ALSO

       Any further question: read the readme file or contact us: pierre.peterlongo@inria.fr

AUTHOR

       This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage
       of the program.