-
Notifications
You must be signed in to change notification settings - Fork 2
/
Copy pathfastq_files.html
150 lines (147 loc) · 5.36 KB
/
fastq_files.html
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
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01//EN" "http://www.w3.org/TR/html4/strict.dtd">
<html lang="en">
<head>
<meta content="en-us" http-equiv="Content-Language"/>
<meta content="text/html; charset=utf-8" http-equiv="Content-Type"/>
<meta content="no-cache, no-store, must-revalidate" http-equiv="Cache-Control"/>
<meta content="no-cache" http-equiv="Pragma"/>
<meta content="0" http-equiv="Expires"/>
<title>
allpairs_global command
</title>
<link href="stylesx.css" rel="stylesheet" type="text/css"/>
<style type="text/css">
body.c4 {background-color:#c0c0c0;}
div.c3 {position:absolute; top:45px; left:20px; width:830px; background-color:#ffffff; border-width:10px; border-style:solid;border-color:white;}
span.c2 {font-weight: bold}
div.c1 {position:absolute; top:10px; left:20px; width:850px; height:60px;}
.TopButtonPara { color:white; background-color:rgb(50,100,150); border-color:rgb(50,100,150); font-family:Arial, Helvetica, sans-serif; font-weight:normal; font-size:9pt; text-align:center; border-width:4px; border-style:solid; }
.TopButton { color:white; }
a.TopButton:link { text-decoration:none; }
a.TopButton:visited { text-decoration:none; }
a.TopButton:hover { color:orange; }
.NewButtonPara { color:white; background-color:rgb(50,100,150); border-color:rgb(50,100,150); font-family:Arial, Helvetica, sans-serif; font-weight:normal; font-size:9pt; text-align:center; border-width:4px; border-style:solid; }
.NewButton { color:white; }
a.NewButton:link { text-decoration:none; }
a.NewButton:visited { text-decoration:none; }
a.NewButton:hover { color:orange; }
.SideButtonPara { color:white; font-family:Arial, Helvetica, sans-serif; font-size:9pt; font-weight:normal; text-align:center; line-height:18px; }
.SideButton { color:white; }
a.SideButton:link { text-decoration:none; }
a.SideButton:visited { text-decoration:none; }
a.SideButton:hover { color:orange; }
</style>
</head>
<body style="background-color:#c0c0c0;">
<div>
<a href="https://drive5.com/usearch">
<img alt="USEARCH v12" src="usearch12_banner.jpg" style="position:absolute; top:40px; left:10px; padding:0px; border:0px;"/>
</a>
</div>
<div style="position:absolute; top:115px; left:10px; width:850px; background-color:#ffffff; min-height:500px">
<div style="position:relative; float:left; background-color:#696969; width:125px; left: 0px; min-height:500px; padding:5px; height: 125px;">
<div class="SideButtonPara" style="text-align:center; padding-top:5px;">
<a class="SideButton" href="index.html">
Docs home
</a>
<br/>
<hr style="border:0; border-bottom: 1px solid white;"/>
<a class="SideButton" href="cmds.html">
Commands
</a>
<br/>
<a class="SideButton" href="topics.html">
Topics
</a>
<br/>
<a class="SideButton" href="citation.html">
Publications
</a>
<br/>
</div>
</div>
<div class="ManText" style="left:20px; position: absolute; left:135px; width:695px; background-color:white; padding:10px">
<h1>
FASTQ files
</h1>
<span class="ManText">
<b>
See also
<br/>
</b>
<a href="quality_score.html">
Quality scores
</a>
<br/>
<b>
</b>
<a href="avgq.html">
Average Q is a bad idea!
</a>
<br/>
<b>
</b>
<a href="fastq_params.html">
FASTQ format options
</a>
<b>
<br/>
</b>
<a href="http://en.wikipedia.org/wiki/FASTQ_format">
Wikipedia article on FASTQ
</a>
<br/>
<a href="exp_errs.html">
Expected errors
</a>
<br/>
<a href="http://www.ncbi.nlm.nih.gov/pubmed?term=20015970">
Cock
<i>
et ail
</i>
(2010) paper describing FASTQ
</a>
<br/>
<br/>
FASTQ files are text files containing sequence data with a
<a href="quality_score.html">
quality (Phred) score
</a>
for each base, represented as an ASCII character. The quality score is an integer (Q) which is typically in the range 2 - 40, but higher and lower values are sometimes used. In particular, versions 1.8 and later of the Illumina platform generate reads with Q scores up to 41.
</span>
<p>
<span class="ManText">
Unfortunately, the FASTQ format is not standardized. There are several variants in common use, and it is not possible to distinguish them automatically with high reliability. The
<a href="DELETE_URL">
fastq_chars
</a>
command can be used to guess the format of an unknown file. See
<a href="fastq_params.html">
FASTQ format options
</a>
.
</span>
</p>
<p align="left">
<img alt="Image" border="1" height="311" src="fastq_fig.jpg" width="553"/>
<br/>
<span class="ManIndText">
<b>
FASTQ read with 50 base calls in Illumina format (ASCII_BASE=33).
<br/>
</b>
There are always four lines per read. The first line starts with '@', followed by the label.
<br/>
The third line starts with '+'. In some variants, the '+' line contains a second copy of the label.
<b>
<br/>
</b>
The fourth line contains the Q scores represented as ASCII characters.
<br/>
</span>
</p>
</div>
</div>
</body>
</html>