基于WGS和CBC测序策略的DNA序列拼接算法研究（六）

4.3.1  程序的结构

Atlas-prep-read

1．create index file

atlas-createindex</perl/bin >(perl程序)

2．split fasta and quality files into 20,000 reads sub files if necessary then screen and trim

       1）atlas-divide-fafile </perl/bin/>(perl程序)

       2）atlas-screen-trim-file</perl/bin>(perl程序)

              A）cross_match</local/>(可执行程序)

              B）atlas-screen-window< /bin >(可执行程序)

3.  32mer count

       1)run_mer_count</perl/lib/PrepRead.pm>(PrepRead.pm包中定义的函数)

       2)find_kmer_peak</perl/lib/PrepRead.pm>(PrepRead.pm包中定义的函数)

       3)eliminate_low_freq</perl/lib/PrepRead.pm>(PrepRead.pm包中定义的函数)

atlas-asm-wgs

1．Run overlapper all vs all

1)run_overlapper</perl/lib/Atlas/AsmWgs.pm>( AsmWgs.pm包中定义的函数)

A) atlas-overlapper< /bin >(可执行程序)

2. run binner

       A) atlas-binner< /bin >(可执行程序)

3.separate bins and run Phrap assembly for each bin

       1)atlas-separate-bin-assemble</perl/bin>( perl程序)

A)read_in_fonfile</perl/lib/Atlas/AsmWgs.pm>(AsmWgs.pm包中定义的函数)

B)mk_bin_dirs</perl/lib/Atlas/AsmWgs.pm>( AsmWgs.pm包中定义的函数)

(I)extract_bin_file</perl/lib/Atlas/AsmWgs.pm>(AsmWgs.pm包中定义的函数)

                            (a)   atlas-extractbins</bin>(可执行程序)

(II)run_asm_bin</perl/lib/Atlas/AsmWgs.pm>(AsmWgs.pm包中定义的函数)

                            (a)   cross_match</local/>(可执行程序)

                            (b)   atlas-screen-window< /bin >(可执行程序)

                            (c)   Phrap</local>(可执行程序)

4. combine ace and contig files and run scaffold

       1) atlas-build-scaffold-file</perl/bin>( perl程序)

              A) create a scaffold object first

              B) build the internal graph structure for the project

              C) delete some edges

              D) add 50kb stuff in

              E) fit gap

              F) delete some edges

              G) bac end pairs

              以上各个阶段都调用了/perl/lib/Atlas/Scaffold.pm中定义的一系列函数。

 

4.3.2  程序的运行流程

 

原始数据通过trimming和k-mer过程以后，送给overlapper进行处理，同时对原始的数据进行索引。Binner程序把overlapper的结果编成bin文件，然后使用Extract把这些bin文件中的序列片段提取出来（这里就利用了前面的所构造的索引）。把这些read送到Phrap中完成局部的拼接，形成contigs