idba_hybrid1
Iterative de bruijn graph assembler for hybrid sequencing data.
Usage
idba_hybrid -r
read.fa
-o
output_dir
[--reference
ref.fa]
Overview
IDBA-Hybrid - Iterative de Bruijn Graph Assembler for hybrid sequencing data.
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)
-
--reference arg -
reference genome
|
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 |
|
minimum size of region in reference genome |
|
similarity for alignment |
|
max mismatch of error correction |
|
minimum number of pairs |
|
maximum gap in reference |
-
--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
6 releases since Debian 8 (Jessie); the text changed 2 times.