idba_ud1
Iterative de bruijn graph assembler for sequencing data with highly uneven depth.
Usage
idba_ud -r
read.fa
-o
output_dir
Overview
IDBA-UD - Iterative de Bruijn Graph Assembler for sequencing data with highly uneven depth.
Allowed Options:
-o,--outarg (=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)
|
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 |
-
--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
Releases
4 releases since Debian 10 (Buster); the text changed 1 time.