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IVA_QC(1) User Commands IVA_QC(1)

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:

Name of assembly fasta file to be compared to reference
Prefix to use for name of all output files

options:

show this help message and exit

Reference options (REQUIRED: either --embl_dir or --ref_db):

Directory of reference EMBL files. If not used, must use --ref_db
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)):

Name of forwards reads fasta or fastq file. Must be used with --reads_rev
Name of reverse reads fasta or fastq file. Must be used with --reads_rev
Name of interleaved fasta/q file

MUMmer options:

Minimum hit length when running nucmer of CDS sequences against contigs [30]
Minimum hit percent identity when running nucmer of CDS sequences against contigs [80]
Minimum hit length when running nucmer of contigs against reference [100]
Minimum hit percent identity when running nucmer of contigs against reference [80]

SMALT mapping options:

kmer hash length in SMALT (the -k option in smalt index) [15]
kmer hash step size in SMALT (the -s option in smalt index) [3]
Minimum identity threshold for mapping to be reported (the -y option in smalt map) [0.5]

External tools:

Minimum percent identity used when GAGE runs nucmer [80]
Use the --preload option when running kraken
Specify your own RATT config file [None]

Other options:

Title to use in contig layout plot [IVA QC contig layout and read depth]
Minimum read coverage of the reference, on each strand, to count as OK coverage [5]
Do not clean temporary files
Number of threads to use [1]
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.

February 2024 iva_qc 1.0.8