NAME

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

SYNOPSIS

       idba_ud -r read.fa -o output_dir

DESCRIPTION

       IDBA-UD - Iterative de Bruijn Graph Assembler  for  sequencing  data  with  highly  uneven
       depth.

   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 (=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

       --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_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

AUTHOR

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