IDBA_UD(1)

💖 IDBA_UD — bestie edition 💖

okay so. this is the manual page for idba_ud, aka Iterative de Bruijn Graph Assembler for sequencing data with highly uneven depth, sitting pretty in section 1 of the manual. yes the name is a mouthful. yes it's iconic. come sit with me, we're gonna go through the whole thing together 🫶

✨ NAME ✨

idba_ud — Iterative de Bruijn Graph Assembler for sequencing data with highly uneven depth.

no cap, that's the whole vibe. she assembles. she iterates. she handles depths that are all over the place like my sleep schedule 😭

🌸 SYNOPSIS 🌸

idba_ud -r read.fa -o output_dir

that's it. that's the whole thing. give her reads, give her a place to put the output, she goes off 👑

🦋 DESCRIPTION 🦋

IDBA-UD — Iterative de Bruijn Graph Assembler for sequencing data with highly uneven depth. she's built for the messy stuff, the data where coverage is like... wildly uneven. lowkey her whole personality.

💅 Allowed Options:

okay here's the full menu, no skipping, every single one of them:

• -o, --out arg (=out) — the output directory. where all the goods land. defaults to out.
• -r, --read arg — fasta read file (<=128). the main character input, fr fr.
• --read_level_2 arg — paired-end reads fasta for second level scaffolds.
• --read_level_3 arg — paired-end reads fasta for third level scaffolds.
• --read_level_4 arg — paired-end reads fasta for fourth level scaffolds.
• --read_level_5 arg — paired-end reads fasta for fifth level scaffolds.
• -l, --long_read arg — fasta long read file (>128). yes she takes the long ones too 💜
• --mink arg (=20) — minimum k value (<=124).
• --maxk arg (=100) — maximum k value (<=124).
• --step arg (=20) — increment of k-mer of each iteration.
• --inner_mink arg (=10) — inner minimum k value.
• --inner_step arg (=5) — inner increment of k-mer.
• --prefix arg (=3) — prefix length used to build sub k-mer table.
• --min_count arg (=2) — minimum multiplicity for filtering k-mer when building the graph.
• --min_support arg (=1) — minimum supoort in each iteration. (yes that's spelled "supoort" in the original, i am NOT touching it, it's her little quirk 🎀)
• --num_threads arg (=0) — number of threads. let her multitask.
• --seed_kmer arg (=30) — seed kmer size for alignment.
• --min_contig arg (=200) — minimum size of contig.
• --similar arg (=0.95) — similarity for alignment.
• --max_mismatch arg (=3) — max mismatch of error correction.
• --min_pairs arg (=3) — minimum number of pairs.
• --no_bubble — do not merge bubble.
• --no_local — do not use local assembly.
• --no_coverage — do not iterate on coverage.
• --no_correct — do not do correction.
• --pre_correction — perform pre-correction before assembly.

lowkey a serve. highkey a serve. the --no_* flags are literally just "bestie, don't do this one thing" and honestly? respect.

👑 AUTHOR 👑

This manpage was written by Andreas Tille for the Debian distribution and can be used for any other usage of the program.

and that's the whole page, bestie, we ate 💅✨

idba_ud version 1.1.3, dated March 2020. mwah. go assemble something gorgeous 🌈🦋💖