surankco-feature - feature generation from contigs and
corresponding reads
surankco-feature [options]
Feature generation from contigs (ACE format) and corresponding
reads (QUAL or FASTQ format).
-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
This manpage was written by Andreas Tille for the Debian
distribution and can be used for any other usage of the program.