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.