idba_hybrid -r read.fa -o output_dir [--reference ref.fa]


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.


-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


do not use local assembly


do not iterate on coverage


do not do correction


perform pre-correction before assembly