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.

surankco-feature 0.0.r5                            March 2016                                SURANKCO-FEATURE(1)