iva_qc options

Required: reads

You must give paired reads either as two separate files with

-f reads_1.fastq -r reads_2.fastq

or in a single interleaved file with

--fr reads.fastq

Required: reference information

You have to either provide a reference genome in the form of a directory of EMBL files with

--embl_dir Directory_name/

or you can provide a database of reference genomes with

--ref_db Database_dir/

You can use iva_qc_make_ref_db to make a reference database. See this page for help.

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Other options

--noclean

Do not clean temporary files

--threads INT

Number of threads to use when running SMALT. Default: 1.

--version

Show program's version number and exit.

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Advanced: MUMmer

--ctg_min_hit_length INT

Minimum hit length when running nucmer of contigs against reference. Default: 100.

--ctg_min_hit_id FLOAT

Minimum hit percent identity when running nucmer of contigs against reference. Default: 80.

--cds_min_hit_length INT

Minimum hit length when running nucmer of CDS sequences against contigs. Default: 30.

--cds_min_hit_id FLOAT

Minimum hit percent identity when running nucmer of CDS sequences against contigs. Default: 80.

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Advanced: external tools

--gage_minid INT in [0,100]

Minimum percent identity used when GAGE runs nucmer Default: 80.

--kraken_preload

Use the --preload option when running kraken. Only applies if --ref_db is used.

--ratt_config filename

Specify your own RATT config file, instead of the one that is bundled with IVA. If you want to find this file, read the description of this option in your terminal when running this script with --help.

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Advanced: SMALT

These options are used to change the mapping settings when the reads are mapped to each of the reference genome and assembly.

--smalt_k INT or -l INT

kmer hash length in SMALT (the -k option in smalt index). Default: 15.

--smalt_s INTor-s INT`

kmer hash step size in SMALT (the -s option in smalt index). Default: 3.

--smalt_id FLOAT or -y FLOAT

Minimum identity threshold for mapping to be reported (the -y option in smalt map). Default: 0.5

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Advanced: other options

--ctg_layout_plot_title STRING

Title to use in contig layout plot. Put it in quotes. Default: "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. Default: 5