NAME¶

SYNOPSIS¶

DESCRIPTION¶

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¶