Scroll to navigation

SURANKCO-FEATURE(1) User Commands SURANKCO-FEATURE(1)

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.
March 2016 surankco-feature 0.0.r5