surankco-score1
Alignment of contigs and reference genomes and score calculation
Usage
surankco-score [options]
Overview
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
Releases
Unchanged in 5 releases since Debian 9 (Stretch).