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.