.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.49.3.
.TH IVA_QC "1" "February 2024" "iva_qc 1.0.8" "User Commands"
.SH NAME
iva_qc \- compare an assembly to a reference
.SH DESCRIPTION
usage: iva_qc [options] {(\fB\-f\fR <reads_1.fq> \fB\-r\fR <reads_2.fq>) | \fB\-\-fr\fR reads.fq} {(\fB\-\-embl_dir\fR | \fB\-\-ref_db\fR) <directory>} <assembly.fasta> <prefix of output files>
.SS "positional arguments:"
.TP
assembly.fasta
Name of assembly fasta file to be compared to
reference
.TP
prefix of output files
Prefix to use for name of all output files
.SS "options:"
.TP
\fB\-h\fR, \fB\-\-help\fR
show this help message and exit
.SS "Reference options (REQUIRED: either --embl_dir or --ref_db):"
.TP
\fB\-\-embl_dir\fR Directory
Directory of reference EMBL files. If not used, must
use \fB\-\-ref_db\fR
.TP
\fB\-\-ref_db\fR Directory
Directory of database made by iva_qc_make_db. If not
used, must use \fB\-\-embl_dir\fR
.SS "Reads options (REQUIRED: either --fr, or (-f and -r)):"
.TP
\fB\-f\fR filename[.gz], \fB\-\-reads_fwd\fR filename[.gz]
Name of forwards reads fasta or fastq file. Must be
used with \fB\-\-reads_rev\fR
.TP
\fB\-r\fR filename[.gz], \fB\-\-reads_rev\fR filename[.gz]
Name of reverse reads fasta or fastq file. Must be
used with \fB\-\-reads_rev\fR
.TP
\fB\-\-fr\fR filename[.gz]
Name of interleaved fasta/q file
.SS "MUMmer options:"
.TP
\fB\-\-cds_min_hit_length\fR INT
Minimum hit length when running nucmer of CDS
sequences against contigs [30]
.TP
\fB\-\-cds_min_hit_id\fR FLOAT
Minimum hit percent identity when running nucmer of
CDS sequences against contigs [80]
.TP
\fB\-\-ctg_min_hit_length\fR INT
Minimum hit length when running nucmer of contigs
against reference [100]
.TP
\fB\-\-ctg_min_hit_id\fR FLOAT
Minimum hit percent identity when running nucmer of
contigs against reference [80]
.SS "SMALT mapping options:"
.TP
\fB\-k\fR INT, \fB\-\-smalt_k\fR INT
kmer hash length in SMALT (the \fB\-k\fR option in smalt
index) [15]
.TP
\fB\-s\fR INT, \fB\-\-smalt_s\fR INT
kmer hash step size in SMALT (the \fB\-s\fR option in smalt
index) [3]
.TP
\fB\-y\fR FLOAT, \fB\-\-smalt_id\fR FLOAT
Minimum identity threshold for mapping to be reported
(the \fB\-y\fR option in smalt map) [0.5]
.SS "External tools:"
.TP
\fB\-\-gage_minid\fR INT in [0,100]
Minimum percent identity used when GAGE runs nucmer
[80]
.TP
\fB\-\-kraken_preload\fR
Use the \fB\-\-preload\fR option when running kraken
.TP
\fB\-\-ratt_config\fR filename
Specify your own RATT config file [None]
.SS "Other options:"
.TP
\fB\-\-ctg_layout_plot_title\fR STRING
Title to use in contig layout plot [IVA QC contig
layout and read depth]
.TP
\fB\-\-min_ref_cov\fR INT
Minimum read coverage of the reference, on each
strand, to count as OK coverage [5]
.TP
\fB\-\-noclean\fR
Do not clean temporary files
.TP
\fB\-\-threads\fR INT
Number of threads to use [1]
.TP
\fB\-\-version\fR
show program's version number and exit
.PP
You must supply reads in one of two ways: 1) both \fB\-\-reads_fwd\fR and \fB\-\-reads_rev\fR;
or 2) \fB\-\-fr\fR. Also, you must either supply a reference with \fB\-\-embl_dir\fR, or
choose one automatically from a database with \fB\-\-ref_db\fR.