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专业背景：计算机科学研究方向与兴趣: JavaEE-Web软件开发, 生物信息学, 数据挖掘与机器学习, 智能信息系统目前工作: 基因组, 转录组, NGS高通量数据分析, 生物数据挖掘, 植物系统发育和比较进化基因组学

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新一代测序技术（NGS）组装简介一

2010-01-01 11:12:59| 分类：生物信息学 | 标签： |举报 |字号大中小订阅

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实用的贴士：

* 概述

Illumina 和 Sanger 的fastq 有着不同的ASCII质量值表，如下：

FASTQ格式:

@HWI-EAS59:1:1:0:899#0/1

NAGTAAATCCCTACTTGAATTCGAGCACTGCAACAAACTA

+HWI-EAS59:1:1:0:899#0/1

DNWWZYPYZMKNYS[SBBBBBBBBBBBBBBBBBBBBBBBB

@HWI-EAS59:1:1:1:449#0/1

NGGGAATGATTAATTCCACAAAACAAAAGAAAGAAGTCGG

+HWI-EAS59:1:1:1:449#0/1

DIZZZ[YXS[U[XTWYTXXXRQLGY[YWPPZSXY[BBBBB

@HWI-EAS59:1:1:1:1018#0/1

NGTAGATAAAAAAATAAACTCAAATAAATTAAAGAGAATC

+HWI-EAS59:1:1:1:1018#0/1

DMPTQS[XYYZ[QQQOMJQLRTSWBBBBBBBBBBBBBBBB

@HWI-EAS59:1:1:1:805#0/1

NAGTATGCTATATTATGATATGTTATGAGATGTTATGTTT

+HWI-EAS59:1:1:1:805#0/1

DNUOMJTTXRRLYOBBBBBBBBBBBBBBBBBBBBBBBBBB

@HWI-EAS59:1:1:1:1371#0/1

AGAGATAGTAAAATCTCATAAATTACTATCAATTCATTCA

+HWI-EAS59:1:1:1:1371#0/1

a\aVb`bZYZ_a`aaP[`TGYTYUaZF_Y`a_W]X[HK^P

@HWI-EAS59:1:1:1:1278#0/1

ATAATAATAAAATATAACTGGTATGTTTATTTATTTATTA

+HWI-EAS59:1:1:1:1278#0/1

``aaaa\a`]]JZaXV`a^VR_^YFFN`a_aGQV_STBBB

@HWI-EAS59:1:1:1:907#0/1

ATAATATCAATAAAAAGAAACAACGACAACCTATAAGCAC

+HWI-EAS59:1:1:1:907#0/1

aba`a_a``]Raaa]ZR^aaa_aTQ_aa\J_WQZKRHK_\

@HWI-EAS59:1:1:1:154#0/1

TGATTAAATGCAAATTTAATTTAAAGAACAGCTGAATAAT

+HWI-EAS59:1:1:1:154#0/1

_^^bb`[U___[aa]`\`VX]a[SFODYWGZbBBBBBBBB

The syntax of Solexa/Illumina read format is almost identical to the FASTQ format, but the qualities are scaled differently. Given a character $sq, the following Perl code gives the Phred quality $Q:

$Q = 10 * log(1 + 10 ** (ord($sq) - 64) / 10.0)) / log(10);

The ASCII charactars in Solexa FASTQ means:

Code:

CHAR DEC QUALITY

A 65 1

B 66 2

C 67 3

D 68 4

E 69 5

F 70 6

G 71 7

H 72 8

I 73 9

J 74 10

K 75 11

L 76 12

M 77 13

N 78 14

O 79 15

P 80 16

Q 81 17

R 82 18

S 83 19

T 84 20

U 85 21

V 86 22

W 87 23

X 88 24

Y 89 25

Z 90 26

[ 91 27

\ 92 28

] 93 29

^ 94 30

_ 95 31

` 96 32

a 97 33

b 98 34

c 99 35

d 100 36

e 101 37

f 102 38

g 103 39

h 104 40

; 59 -5

< 60 -4

= 61 -3

> 62 -2

? 63 -1

@ 64 0

In contrast to Solexa FASTQ quality, the ASCII characters in standard (sanger) FASTQ, it used to denote:

Code:

CHAR DEC QUALITY

! 0 -64

! 1 -63

! 2 -62

! 3 -61

! 4 -60

! 5 -59

! 6 -58

! 7 -57

! 8 -56

! 9 -55

! 10 -54

! 11 -53

! 12 -52

! 13 -51

! 14 -50

! 15 -49

! 16 -48

! 17 -47

! 18 -46

! 19 -45

! 20 -44

! 21 -43

! 22 -42

! 23 -41

! 24 -40

! 25 -39

! 26 -38

! 27 -37

! 28 -36

! 29 -35

! 30 -34

! 31 -33

! 32 -32

! 33 -31

! 34 -30

! 35 -29

! 36 -28

! 37 -27

! 38 -26

! 39 -25

! 40 -24

! 41 -23

! 42 -22

! 43 -21

! 44 -20

! 45 -19

! 46 -18

! 47 -17

! 48 -16

! 49 -15

! 50 -14

! 51 -13

! 52 -12

! 53 -11

! 54 -10

" 55 -9

" 56 -8

" 57 -7

" 58 -6

" 59 -5

" 60 -4

# 61 -3

# 62 -2

$ 63 -1

$ 64 0

% 65 1

% 66 2

& 67 3

& 68 4

' 69 5

( 70 6

) 71 7

* 72 8

+ 73 9

+ 74 10

, 75 11

- 76 12

. 77 13

/ 78 14

0 79 15

1 80 16

2 81 17

3 82 18

4 83 19

5 84 20

6 85 21

7 86 22

8 87 23

9 88 24

: 89 25

; 90 26

< 91 27

= 92 28

> 93 29

? 94 30

@ 95 31

A 96 32

B 97 33

C 98 34

D 99 35

E 100 36

F 101 37

G 102 38

H 103 39

I 104 40

J 105 41

K 106 42

L 107 43

M 108 44

N 109 45

O 110 46

P 111 47

Q 112 48

R 113 49

S 114 50

T 115 51

U 116 52

V 117 53

W 118 54

X 119 55

Y 120 56

Z 121 57

[ 122 58

\ 123 59

] 124 60

^ 125 61

_ 126 62

` 127 63

a 128 64

So it is easy to conver Solexa->Sanger quality, you just need to build a conversion table in PERL script, just like this:

# Solexa->Sanger quality conversion table

my @conv_table;

for (-64..64) {

$conv_table[$_+64] = chr(int(33 + 10*log(1+10**($_/10.0))/log(10)+.499));

}

所以你首先要确定你测序得到的数据是来自什么测序中心和测序技术得到的，并需探讨用什么质控(quality check)和序列修饰(trimming)手段。

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