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.

surankco-score 0.0.r5                              March 2016                                  SURANKCO-SCORE(1)