idba - Online in the Cloud

PROGRAM:

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

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