NAME

       idba - Iterative de Bruijn Graph Assembler for hybrid sequencing data

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