IVA_QC(1)

NAME

okay so bestie, meet iva_qc — a lil User Commands icon whose whole entire job is to compare an assembly to a reference. That's it, that's the mission. 💖

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DESCRIPTION

Here's how you summon her:

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>

Read it slow, she's doing a lot. 🌸

positional arguments:

• assembly.fasta — the name of the assembly fasta file you're comparing to the reference. This is your main character. 👑
• prefix of output files — the prefix used for the name of all your output files. Every single one. Name it wisely. ✨

options:

• -h, --help — shows this help message and dips out. 🫶

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

Pick one, you literally have to — no reference, no results, periodt. 💅

• --embl_dir Directory — a directory of reference EMBL files. If you don't use this one, you must use --ref_db.
• --ref_db Directory — a directory of a database made by iva_qc_make_db. If you don't use this one, you must use --embl_dir.

Reads options (REQUIRED: either --fr, or (-f and -r))

Same energy, but for reads. Give her reads one of two ways, or she's not going anywhere. 😭

• -f filename[.gz], --reads_fwd filename[.gz] — name of the forwards reads fasta or fastq file. Must be used with --reads_rev.
• -r filename[.gz], --reads_rev filename[.gz] — name of the reverse reads fasta or fastq file. Must be used with --reads_rev.
  • not me noticing it says --reads_rev on both of them 🙈 that is literally, word for word, what the page says, and I am not out here editing the source, bestie
• --fr filename[.gz] — name of the interleaved fasta/q file. 🦋

MUMmer options

the nucmer knobs, tuned just how you like 'em.

• --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 the reference [100].
• --ctg_min_hit_id FLOAT — minimum hit percent identity when running nucmer of contigs against the reference [80].

SMALT mapping options

• -k INT, --smalt_k INT — kmer hash length in SMALT (that's the -k option in smalt index) [15].
• -s INT, --smalt_s INT — kmer hash step size in SMALT (that's the -s option in smalt index) [3].
• -y FLOAT, --smalt_id FLOAT — minimum identity threshold for a mapping to be reported (that's 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 — the title to use in the 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 the program's version number and exit. ⭐

okay bestie real talk, read this twice: 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. That's the whole contract. No reads + no reference = nothing happens, and the vibes will be immaculate but empty. 💀

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and that's the page, bestie 🎀 this was iva_qc, version 1.0.8, dated December 2024 — go compare an assembly to a reference and absolutely ate. ✨👑🌈