---
name: "idba"
section: "1"
platform: "linux"
package: "idba"
version: "1.1.3-8"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/idba"
---

# idba(1)

Iterative de Bruijn Graph Assembler

## NAME

idba - Iterative de Bruijn Graph Assembler

## SYNOPSIS

**idba\_ud** *-r read.fa -o output\_dir*

## DESCRIPTION

IDBA- Iterative de Bruijn Graph Assembler.

### Allowed Options:

- **-o**, **--out** arg (=out)

  output directory

- **-r**, **--read** arg

  fasta read file (\<=128)

- **--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)

- **--mink** arg (=20)

  minimum k value (\<=124)

- **--maxk** arg (=50)

  maximum k value (\<=124)

- **--step** arg (=10)

  increment of k-mer of each iteration

- **--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

- **--num\_threads** arg (=0)

  number of threads

- **--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\_coverage**

  do not iterate on coverage

- **--no\_correct**

  do not do correction

- **--pre\_correction**

  perform pre-correction before assembly

## AUTHOR

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