iva_qc(1) 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.