.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.43.3.
.TH IDBA_HYBRID "1" "February 2014" "idba_hybrid 1.1.1" "User Commands"
.SH NAME
idba_hybrid \- Iterative de Bruijn Graph Assembler for hybrid sequencing data
.SH SYNOPSIS
.B idba_hybrid
\fI\-r read.fa \-o output_dir \fR[\fI\-\-reference ref.fa\fR]
.SH 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.
.SH OPTIONS
.TP
\fB\-o\fR, \fB\-\-out\fR arg (=out)
output directory
.TP
\fB\-r\fR, \fB\-\-read\fR arg
fasta read file (<=128)
.TP
\fB\-\-read_level_2\fR arg
paired\-end reads fasta for second level scaffolds
.TP
\fB\-\-read_level_3\fR arg
paired\-end reads fasta for third level scaffolds
.TP
\fB\-\-read_level_4\fR arg
paired\-end reads fasta for fourth level scaffolds
.TP
\fB\-\-read_level_5\fR arg
paired\-end reads fasta for fifth level scaffolds
.TP
\fB\-l\fR, \fB\-\-long_read\fR arg
fasta long read file (>128)
.TP
\fB\-\-reference\fR arg
reference genome
.TP
\fB\-\-mink\fR arg (=20)
minimum k value (<=124)
.TP
\fB\-\-maxk\fR arg (=100)
maximum k value (<=124)
.TP
\fB\-\-step\fR arg (=20)
increment of k\-mer of each iteration
.TP
\fB\-\-inner_mink\fR arg (=10)
inner minimum k value
.TP
\fB\-\-inner_step\fR arg (=5)
inner increment of k\-mer
.TP
\fB\-\-prefix\fR arg (=3)
prefix length used to build sub k\-mer table
.TP
\fB\-\-min_count\fR arg (=2)
minimum multiplicity for filtering k\-mer when building the graph
.TP
\fB\-\-min_support\fR arg (=1)
minimum supoort in each iteration
.TP
\fB\-\-num_threads\fR arg (=0)
number of threads
.TP
\fB\-\-seed_kmer\fR arg (=30)
seed kmer size for alignment
.TP
\fB\-\-min_contig\fR arg (=200)
minimum size of contig
.TP
\fB\-\-min_region\fR arg (=500)
minimum size of region in reference genome
.TP
\fB\-\-similar\fR arg (=0.95)
similarity for alignment
.TP
\fB\-\-max_mismatch\fR arg (=3)
max mismatch of error correction
.TP
\fB\-\-min_pairs\fR arg (=3)
minimum number of pairs
.TP
\fB\-\-max_gap\fR arg (=50)
maximum gap in reference
.TP
\fB\-\-no_local\fR
do not use local assembly
.TP
\fB\-\-no_coverage\fR
do not iterate on coverage
.TP
\fB\-\-no_correct\fR
do not do correction
.TP
\fB\-\-pre_correction\fR
perform pre\-correction before assembly