bionic (1) surankco-feature.1.gz

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.