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

# surankco-feature(1)

feature generation from contigs and corresponding reads

## NAME

surankco-feature - feature generation from contigs and corresponding reads

## SYNOPSIS

**surankco-feature** \[*options*\]

## DESCRIPTION

Feature generation from contigs (ACE format) and corresponding reads (QUAL or FASTQ format).

## OPTIONS

**-a** ASSEMBLIES, **--assemblies**=*ASSEMBLIES*

-

  Indicate a list of assembly files (comma separated), correct suffixes are mandatory (e.g. ".ace")

**-d** DIRECTORY, **--directory**=*DIRECTORY*

-

  Indicate a directory containing assembly files with indicated format (default: ace, see parameter **-f**)

**-f** ASSEMBLY.FORMAT, **--assembly**.format=ASSEMBLY.FORMAT

-

  Indicate assembly/contig format (resp. suffix), either "ace" (default) or "contigs.fasta"

**-r** READ.QUALITY.FORMAT, **--read**.quality.format=READ.QUALITY.FORMAT

-

  Indicate the read quality format: qual, qua or fastq for ACE (default="qual") resp. sam or bam for contigs.fasta (default="sam")

**-q** FASTQ.VERSION, **--fastq**.version=FASTQ.VERSION

-

  Indicate the fastq version: auto, sanger, solexa, illumina13, illumina15, illumina18 (default). Only needed for ACE assemblies.

**-s** SPLIT.REGEX, **--split**.regex=SPLIT.REGEX

-

  Indicate a regular expression to cutoff read names (e.g. if modified by the assembler). Only needed for ACE assemblies. Note, if a backslash "\\" is needed use "\\\\\\\\"!

**-t** THREADS, **--threads**=*THREADS*

-

  Indicate a number of cores or threads to use. Might speed up some parallelized operations (default: 1)

**-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.

**-k**, **--kmer**.features

-

  Indicates whether k-mer features should be computed (experimental, very long runtime) or not (default)

**-g** EXPECTED.GENOME.SIZE, **--expected**.genome.size=EXPECTED.GENOME.SIZE

-

  Indicate a list of expected genome sizes (comma separated) or one value for all assemblies. Default is 0, which will estimate the genome sizes as sum of contig lengths.

**-c** CONTIG.SIZE.FILTER, **--contig**.size.filter=CONTIG.SIZE.FILTER

-

  Indicate a minimum contig size. Default: 0

**-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.