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IDBA_UD(1) User Commands IDBA_UD(1)

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.
March 2020 idba_ud 1.1.3