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.