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.

idba 1.1.3                                         March 2020                                            IDBA(1)