NAME

       run_mapsembler2_pipeline - manual page for run_mapsembler2_pipeline 2.2.4+dfsg

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

              -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)

   <options>:
              -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

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

SEE ALSO

       The  full  documentation for run_mapsembler2_pipeline is maintained as a Texinfo manual.  If the info and
       run_mapsembler2_pipeline programs are properly installed at your site, the command

              info run_mapsembler2_pipeline

       should give you access to the complete manual.

run_mapsembler2_pipeline 2.2.4+dfsg              September 2017                      RUN_MAPSEMBLER2_PIPELINE(1)