idba_hybrid(1) Iterative de Bruijn Graph Assembler for hybrid sequencing data


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