---
name: "iva_qc"
section: "1"
platform: "linux"
package: "iva"
version: "1.0.11+ds-6"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/iva_qc"
---

# iva\_qc(1)

compare an assembly to a reference

## 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:

- 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

### options:

- **-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**.