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SURANKCO-SCORE(1) User Commands SURANKCO-SCORE(1)

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.
March 2016 surankco-score 0.0.r5