Staden

pregap4

Files to process - add files 添加所需要的ab1

File - Load New Configure File - configure

Configure Modules - Run

gap4

一般拼接

File - New 创建数据库

Assembly - Normal shotgun assembly 写以下内容

Input reading filenames from 选择 file

List or file name 选择 pregap4 生成的 *.passed文件

Save failures to 选择 file

List or file name 直接新建

OK

File - Save consensus - normal

Select format 选择 fasta

Output file 新建一个

OK

再次拼接

View - Find internal joins

或者

View - Find repeats

trev

trev ab1file

查看峰图

configure

文件示例

# Config file format version 1.0
[module_list]
set MODULE_PATH {$env(STADTCL)/pregap4/modules }
set MODULES {
	phred
	atqa
	eba
	convert_trace
	compress_trace
	init_exp
	augment_exp
	quality_clip
	sequence_vector_clip
	cross_match_svec
	screen_vector
	polyA
	cloning_vector_clip
	screen_seq
	blast
	interactive_clip
	repeat_masker
	hetins
	reference
	mutscan
	gap4_assemble
	cap3_assemble
	fakii_assemble
	phrap_assemble
	enter_assembly
	email
}

[::init]
set enabled 1
set use_sample_name 0

[::phred]
set enabled 0

[::atqa]
set enabled 0

[::eba]
set enabled 1
set scale logarithmic

[::convert_trace]
set enabled 1
set down_scale 0
set down_scale_range 255
set output_format ctf
set subtract_background 0
set normalise 0
set del_temp_files 1

[::compress_trace]
set enabled 0

[::init_exp]
set enabled 1

[::augment_exp]
set enabled 0

[::quality_clip]
set enabled 1
set clip_mode confidence
set offset 70
set min_extent 0
set max_extent 999999
set min_length 0
set window_length 50
set conf_val 15
set right_win_length 100
set right_num_uncalled 5
set left_win_length 25
set left_num_uncalled 3

[::sequence_vector_clip]
set enabled 1
set use_vp_file 1
set vp_file /usr/bin/../share/staden/etc/vector_primer
set vector_list {}
set vp_length 40
set min_5_match 60
set min_3_match 80
set def_5_pos -1

[global_variables]
set SF {}
set SC {}
set SP {}

[::cross_match_svec]
set enabled 0

[::screen_vector]
set enabled 0

[::polyA]
set enabled 0

[::cloning_vector_clip]
set enabled 0

[::screen_seq]
set enabled 0

[::blast]
set enabled 0

[::interactive_clip]
set enabled 1

[::repeat_masker]
set enabled 0

[::hetins]
set enabled 0

[::reference]
set enabled 0

[::mutscan]
set enabled 0

[::gap4_assemble]
set enabled 0

[::cap3_assemble]
set enabled 0

[::fakii_assemble]
set enabled 0

[::phrap_assemble]
set enabled 0

[::enter_assembly]
set enabled 0

[::email]
set enabled 0

[::shutdown]
set enabled 1