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.