File: idba_ud.1

package info (click to toggle)
idba 1.1.3-3
  • links: PTS, VCS
  • area: main
  • in suites: bullseye, buster, sid
  • size: 2,840 kB
  • sloc: cpp: 36,571; sh: 1,346; makefile: 199; python: 99; perl: 8
file content (88 lines) | stat: -rw-r--r-- 2,067 bytes parent folder | download
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
.\" DO NOT MODIFY THIS FILE!  It was generated by help2man 1.47.4.
.TH IDBA_UD "1" "August 2017" "idba_ud 1.1.3" "User Commands"
.SH NAME
idba_ud \- Iterative de Bruijn Graph Assembler for hybrid sequencing data
.SH SYNOPSIS
.B idba_ud
\fI\,-r read.fa -o output_dir\/\fR
.SH DESCRIPTION
IDBA\-UD \- Iterative de Bruijn Graph Assembler for sequencing data with highly uneven depth.
.SS "Allowed 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\-\-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\-\-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\-\-no_bubble\fR
do not merge bubble
.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