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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:

output directory
fasta read file (<=128)
paired-end reads fasta for second level scaffolds
paired-end reads fasta for third level scaffolds
paired-end reads fasta for fourth level scaffolds
paired-end reads fasta for fifth level scaffolds
fasta long read file (>128)
minimum k value (<=124)
maximum k value (<=124)
increment of k-mer of each iteration
inner minimum k value
inner increment of k-mer
prefix length used to build sub k-mer table
minimum multiplicity for filtering k-mer when building the graph
minimum supoort in each iteration
number of threads
seed kmer size for alignment
minimum size of contig
similarity for alignment
max mismatch of error correction
minimum number of pairs
do not merge bubble
do not use local assembly
do not iterate on coverage
do not do 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