---
name: "surankco-score"
section: "1"
platform: "linux"
package: "surankco"
version: "0.0.r5+dfsg-4"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/surankco-score"
---

# surankco-score(1)

alignment of contigs and reference genomes and score calculation

## 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.