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.