IDBA

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.