surankco-score(1) 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.