surankco-feature(1) 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)
Indicate assembly/contig format (resp. suffix), either "ace" (default) or "contigs.fasta"
Indicate the read quality format: qual, qua or fastq for ACE (default="qual") resp. sam or bam for contigs.fasta (default="sam")
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)
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.
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.