NAME¶
idba_hybrid - Iterative de Bruijn Graph Assembler for hybrid sequencing data
SYNOPSIS¶
idba_hybrid -r read.fa -o output_dir [
--reference ref.fa]
DESCRIPTION¶
IDBA-Tran is an iterative De Bruijn Graph De Novo short read assembler for
transcriptome. It is purely de novo assembler based on only RNA sequencing
reads. IDBA-Tran uses local assembly to reconstructing missing k-mers in
low-expressed transcripts and then employs progressive cutoff on contigs to
separate the graph into components. Each component corresponds to one gene in
most cases and contains not many transcripts. A heuristic algorithm based on
pair-end reads is then used to find the isoforms.
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)
- --reference arg
- reference genome
- --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
- --min_region arg (=500)
- minimum size of region in reference genome
- --similar arg (=0.95)
- similarity for alignment
- --max_mismatch arg (=3)
- max mismatch of error correction
- --min_pairs arg (=3)
- minimum number of pairs
- --max_gap arg (=50)
- 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