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.