Usage:
    deconseq [options] -f <file> -dbs <list> -dbs_retain <list> ...

Options:
    -help | -h
            Prints the help message and exists.

    -man    Prints the full documentation.

    -version
            Prints the version of the program.

    -show_dbs
            Prints a list of available databases.

    -f <file>
            Input file in FASTA or FASTQ format that contains the query
            sequences.

    -dbs <list>
            Name of database(s) to use (default: hsref). Names are according
            to their definition in the config file. Separate multiple
            database names by comma without spaces.

            Example: -dbs hs1,hs2,hsref

    -dbs_retain <list>
            Name of database(s) to use for cross-check. Query sequences with
            hit against any dbs will be compared to these databases.
            Databases have to be different from names in dbs. Names are
            according to their definition in the config file. Separate
            multiple database names by comma without spaces.

            Example: -dbs_retain bact,vir

    -out_dir <dir>
            Directory where the results should be written (default: .). If
            the directory does not exist, it will be created.

    -i <integer>
            Alignment identity threshold in percentage (integer from 1-100
            without %) used to define matching sequences as similar. The
            identity is calculated for the part of the query sequence that
            is aligned to a reference sequence. For example, a query
            sequence of 100 bp that aligns to a reference sequence over the
            first 50 bp with 40 matching positions has an identity value of
            80%.

    -c <integer>
            Alignment coverage threshold in percentage (integer from 1-100
            without %) used to define matching sequences as similar. The
            coverage is calculated for the part of the query sequence that
            is aligned to a reference sequence. For example, a query
            sequence of 100 bp that aligns to a reference sequence over the
            first 50 bp with 40 matching positions has an coverage value of
            50%.

    -group <integer>
            If dbs_retain is set, then this option can be used to group the
            sequences similar to dbs and dbs_retain databases with either
            the clean or the contamination output file. If group is not set
            and dbs_retain is set, then three separate files will be
            generated.

            Use -group 1 for grouping "Clean + Both" and use -group 2 for
            grouping "Contamination + Both".

    -no_seq_out
            Prevents the generation of the fasta/fastq output file for the
            given coverage and identity thresholds. This feature is e.g.
            useful for the web-version since -i and -c are set interactively
            and not yet defined at the data processing step.

    -keep_tmp_files
            Prevents from unlinking the generated tmp files. These usually
            include the id file and the .tsv file(s). This feature is e.g.
            useful for the web-version since .tsv files are used to
            dynamically generate the output files.

    -id <string>
            Optional parameter. If not set, ID will be automatically
            generated to prevent from overwriting previous results. This
            option is useful if integrated into other tools and the output
            filenames need to be known.

    -S <integer>
            Chunk size of reads in bp as used by BWA-SW (default: 10000000).

    -z <integer>
            Z-best value as used by BWA-SW (default: 1).

    -T <integer>
            Alignment score threshold as used by BWA-SW (default: 30).