NAME

       surankco-score - alignment of contigs and reference genomes and score calculation

SYNOPSIS

       surankco-score [options]

DESCRIPTION

       Alignment  of  contigs  (FASTA  format)  and  reference  genomes  (FASTA format) and score
       calculation

OPTIONS

       -a ASSEMBLIES, --assemblies=ASSEMBLIES

              Indicate a list of assembly files (comma separated), correct suffixes are mandatory
              (default "*.contigs.fasta")

       -d DIRECTORY, --directory=DIRECTORY

              Indicate  a  directory  containing  assembly  files  with  indicated  format  (e.g.
              "*.contigs.fasta")

       -f ASSEMBLY.SUFFIX, --assembly.suffix=ASSEMBLY.SUFFIX

              Indicate assembly format/suffix, default="contigs.fasta"

       -r REFERENCE.SUFFIX, --reference.suffix=REFERENCE.SUFFIX

              Indicate the reference format/suffix, default="ref.fasta"

       -p PDF.HISTOGRAMS, --pdf.histograms=PDF.HISTOGRAMS

              Indicate    a    name    for    the    score    histogram    pdf     (default     =
              "surankco_score_histograms.pdf")

       -m MEMORY, --memory=MEMORY

              Indicate  the  maximum memory usage (in Gb) of Javas virtual machine (default: 32).
              Try to increase if big data sets report heap space problems.

       -h, --help

              Show this help message and exit

AUTHOR

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