NAME

       iva_qc - compare an assembly to a reference

DESCRIPTION

       usage: iva_qc [options] {(-f <reads_1.fq> -r <reads_2.fq>) | --fr reads.fq} {(--embl_dir |
       --ref_db) <directory>} <assembly.fasta> <prefix of output files>

   positional arguments:
       assembly.fasta
              Name of assembly fasta file to be compared to reference

       prefix of output files
              Prefix to use for name of all output files

   optional arguments:
       -h, --help
              show this help message and exit

   Reference options (REQUIRED: either --embl_dir or --ref_db):
       --embl_dir Directory
              Directory of reference EMBL files. If not used, must use --ref_db

       --ref_db Directory
              Directory of database made by iva_qc_make_db. If not used, must use --embl_dir

   Reads options (REQUIRED: either --fr, or (-f and -r)):
       -f filename[.gz], --reads_fwd filename[.gz]
              Name of forwards reads fasta or fastq file. Must be used with --reads_rev

       -r filename[.gz], --reads_rev filename[.gz]
              Name of reverse reads fasta or fastq file. Must be used with --reads_rev

       --fr filename[.gz]
              Name of interleaved fasta/q file

   MUMmer options:
       --cds_min_hit_length INT
              Minimum hit length when running nucmer of CDS sequences against contigs [30]

       --cds_min_hit_id FLOAT
              Minimum hit percent identity when running nucmer of CDS sequences  against  contigs
              [80]

       --ctg_min_hit_length INT
              Minimum hit length when running nucmer of contigs against reference [100]

       --ctg_min_hit_id FLOAT
              Minimum hit percent identity when running nucmer of contigs against reference [80]

   SMALT mapping options:
       -k INT, --smalt_k INT
              kmer hash length in SMALT (the -k option in smalt index) [15]

       -s INT, --smalt_s INT
              kmer hash step size in SMALT (the -s option in smalt index) [3]

       -y FLOAT, --smalt_id FLOAT
              Minimum  identity threshold for mapping to be reported (the -y option in smalt map)
              [0.5]

   External tools:
       --gage_minid INT in [0,100]
              Minimum percent identity used when GAGE runs nucmer [80]

       --kraken_preload
              Use the --preload option when running kraken

       --ratt_config filename
              Specify your own RATT config file [None]

   Other options:
       --ctg_layout_plot_title STRING
              Title to use in contig layout plot [IVA QC contig layout and read depth]

       --min_ref_cov INT
              Minimum read coverage of the reference, on each strand, to count as OK coverage [5]

       --noclean
              Do not clean temporary files

       --threads INT
              Number of threads to use [1]

       --version
              show program's version number and exit

       You must supply reads in one of two ways: 1) both --reads_fwd and --reads_rev; or 2) --fr.
       Also, you must either supply a reference with --embl_dir, or choose one automatically from
       a database with --ref_db.