IVA(1)

📦
version 1.0.11 · 6 versions
, in debian trixie, ubuntu questing

💖 IVA(1) — the iva era 💖

okay bestie, sit DOWN, because we're talking about iva, the iterative virus assembler. yes, that's the whole name. short, sweet, iconic, does exactly what it says on the tin. 🦋

✨ NAME ✨

iva — iterative virus assembler 👑

🌸 DESCRIPTION 🌸

the vibe is simple, fr fr:

usage: iva [options] {-f reads_fwd -r reads_rev | --fr reads} <output directory>

so like. you give it reads, it gives you contigs. that's the whole main character arc. 💅

🎀 positional arguments 🎀

  • Output directory — this is the name of the output directory. and bestie, listen: it must not already exist. no pre-made folders, no "I'll just make it real quick", nothing. let iva birth it itself. 🙈

🧚 options 🧚

  • -h, --help — show this help message and exit. the classic. the beloved. the "wait what does this do again" button. 💖

🍓 Input and output 🍓

  • -f filename[.gz], --reads_fwd filename[.gz] — name of the forward reads fasta/q file. you literally cannot use this alone, it has to be used in conjunction with --reads_rev. they're a package deal, a duo, a ship. 🫶
  • -r filename[.gz], --reads_rev filename[.gz] — name of the reverse reads fasta/q file. same deal: must be used in conjunction with --reads_fwd. no solo careers here. ✨
  • --fr filename[.gz] — name of the interleaved fasta/q file. one file, both directions, efficiency queen. 👑
  • --keep_files — keep intermediate files. and when I say files I mean it could be many, like genuinely a lot. the default is to delete all the unnecessary ones, so only reach for this if you actually want the clutter. 🗂️
  • --contigs filename[.gz] — fasta file of contigs to be extended. incompatible with --reference, so pick a lane bestie. 🚫
  • --reference filename[.gz] — ⚠️ EXPERIMENTAL! this option is EXPERIMENTAL, not recommended, and has not been tested! it's a fasta file of a reference genome, or parts thereof. IVA will try to assemble one contig per sequence in this file. also incompatible with --contigs. like, it's giving "we put it here but please don't". 💀
  • -v, --verbose — be verbose by printing messages to stdout. and the fun part: use it up to three times for increasing verbosity. stack them. go feral. 🔥

🌈 SMALT mapping options 🌈

  • -k INT, --smalt_k INT — kmer hash length in SMALT, aka the -k option in smalt index [19]. 🧬
  • -s INT, --smalt_s INT — kmer hash step size in SMALT, aka the -s option in smalt index [11]. 👟
  • -y FLOAT, --smalt_id FLOAT — minimum identity threshold for a mapping to be reported, aka the -y option in smalt map [0.5]. no mid mappings allowed. 💅

🦋 Contig options 🦋

  • --ctg_first_trim INT — number of bases to trim off the end of every contig before extending for the first time [25]. fresh start energy. ✂️
  • --ctg_iter_trim INT — during iterative extension, the number of bases to trim off the end of a contig when extension fails (and then it tries extending again) [10]. it's giving "okay that didn't work, let me just… adjust". 😭
  • --ext_min_cov INT — minimum kmer depth needed to use that kmer to extend a contig [10]. 📏
  • --ext_min_ratio FLOAT — sets N, where the kmer for extension must be at least N times more abundant than the next most common kmer [4]. popular kmer wins. 👑
  • --ext_max_bases INT — maximum number of bases to try to extend on each iteration [100]. know your limits. 🛑
  • --ext_min_clip INT — set the minimum number of bases soft clipped off a read for those bases to be used for extension [3]. 🪄
  • --max_contigs INT — maximum number of contigs allowed in the assembly. no more seeds are generated once the cutoff is reached [50]. capacity reached, we're full. 🎟️

🧬 Seed generation options 🧬

  • --make_new_seeds — when no more contigs can be extended, generate a new seed. this is forced to be true when --contigs is not used. no takebacks. 🌱
  • --seed_start_length INT — when making a seed sequence, use the most common kmer of this length. the default is to use the minimum of (median read length, 95). ⚠️ warning: it is not recommended to set this higher than 95. 📐
  • --seed_stop_length INT — stop extending the seed using perfect matches from reads when this length is reached. future extensions are then made by treating the seed as a contig [0.9*max_insert]. graduation day. 🎓
  • --seed_min_kmer_cov INT — minimum kmer coverage of the initial seed [25]. 🪴
  • --seed_max_kmer_cov INT — maximum kmer coverage of the initial seed [1000000]. a whole million, no cap. 🤯
  • --seed_ext_max_bases INT — maximum number of bases to try to extend on each iteration [50]. 🚧
  • --seed_overlap_length INT — number of overlapping bases needed between a read and the seed to use that read to extend [seed_start_length]. we need some common ground first. 🤝
  • --seed_ext_min_cov INT — minimum kmer depth needed to use that kmer to extend a contig [10]. 📊
  • --seed_ext_min_ratio FLOAT — sets N, where the kmer for extension must be at least N times more abundant than the next most common kmer [4]. same energy, seed edition. ✨

🎀 Read trimming options 🎀

  • --trimmomatic FILENAME — provide the location of the trimmomatic.jar file to enable read trimming. required if --adapters is used. 🧹
  • --trimmo_qual STRING — trimmomatic options used to quality trim reads [LEADING:10 TRAILING:10 SLIDINGWINDOW:4:20]. 🧼
  • --adapters FILENAME — fasta file of adapter sequences to be trimmed off reads. if you use this, you must also use --trimmomatic. the default is the file of adapters supplied with IVA. ✂️
  • --min_trimmed_length INT — minimum length of a read after trimming [50]. short king gets dropped. 📉
  • --pcr_primers FILENAME — FASTA file of primers. the first perfect match found to a sequence in the primers file will be trimmed off the start of each read. this runs after trimmomatic (if --trimmomatic is used). 🧪

💜 Other options 💜

  • -i INT, --max_insert INT — maximum insert size, and yes, that includes read length. reads with an inferred insert size more than the maximum will not be used to extend contigs [800]. too far, not invited. 🚫
  • -t INT, --threads INT — number of threads to use [1]. give it more, let it cook. 🔥
  • --kmc_onethread — force kmc to use one thread. by default the value of -t/--threads is used when running kmc. so this is your "actually no, just one" override. ☝️
  • --strand_bias FLOAT in [0,0.5] — set the strand bias cutoff of mapped reads when trimming contig ends, in the interval [0,0.5]. a value of x means a base needs min(fwd_depth, rev_depth) / total_depth <= x. the only time this should be used is with libraries with overlapping reads (ie fragment length < 2*read length), and even then, it can make results worse. if you use it, try a low value like 0.1 first [0]. seriously bestie, tread carefully. ⚠️
  • --test — run using built in test data. all other options will be ignored, except the mandatory output directory, and --trimmomatic and --threads can also be used. it's the "just show me it works" button. 🧸
  • --version — show program's version number and exit. 📜
lowkey the whole thing is just: give it reads, tell it where to put the output, and let it iterate. highkey iconic. 👑

and that's the tea. this page is iva 1.0.8, from December 2024, part of the IVA(1) family. go assemble something gorgeous bestie 💖✨🦋

📦 where this page comes from