Bacterial Genome Data mining & Bioinformatic Analysis
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Batch-ANIm: fast to calcutate genome average nucleotide identity (ANI) using jspecies with multiple threads

Batch-ANIm由ANI计算软件Jspecies和多个功能程序脚本组成。该软件通过Aspera高速完成大量基因组序列下载,平行启动多个Jspecies程序并自动完成两两基因组配对和序列导入,能够快速计算获得大量基因组两两之间ANI值。使用方法详见http://www.microbialgenomic.com/Batch-ANIm.html

如果使用Batch-ANIm,请引用一下参考文献: Batch-ANIm:平均核苷酸相似度快速计算工具分析无色杆菌属菌株亲缘关系(待发表)

Batch_ANI下载地址: Batch-ANIm.tar.gz
 
使用说明

 

1. Installation of required Perl modules, R packages and programs
===================================================================================

But before running, Batch-ANI needs to pre-install Java, Aspera, Mummer, several Perl Modules,and R packages. In addition, the paths of workplace and mummer in Jspecies need to be set.

Perl Modules list:
(1) threads; (2) Getopt::Long;

R packages list:
(1) ape; (2) plotrix;

Jspecies pathway set:
******before using jspecies, the users needs to set the absolute pathway for workplace (recommend to use ANI_direction as workplace), and nucmer manually. Please refer to jspecies usage available at http://imedea.uib-csic.es/jspecies/index.html.******

Aspera install:
******Aspera could be download from https://downloads.asperasoft.com/******

2. Running Batch-ANIm
==============================

******每一个功能里面都包括有详细使用说明******

(1) genome_batch_retrive.pl 采用Aspera高速下载基因组序列数据; 输入文件:每一行包括一个基因组FTP下载地址的文本文档

下载格式说明:用户可以根据需要下载全基因组的注释文件、全全基因组核苷酸序列文件 、全部编码基因核苷酸序列、全部编码基因氨基酸序列

例如:

genomes/all/GCF/001/571/245/GCF_001571245.1_ASM157124v1/GCF_001571245.1_ASM157124v1_genomic.fna.gz 只下载全基因组的核苷酸序列文件

genomes/all/GCF/001/571/245/GCF_001571245.1_ASM157124v1 涵盖所有基因组的数据。

(2)Batch_import_conf.pl 根据菌株名文件列表生成配置文件,平行启动多个Jspecies,并自动完成基因组序列导入和基因组配对选择。 输入文件:(1)含包括多个基因组核苷酸序列文件的文件夹、(2)菌株名文件列表

此步完成之后,将会形成多个ANI计算文件夹,用户需要根据Jspecies图形界面,分别导入基因组序列文件,并选择计算ANIm,计算完成后,需要用户手工保存每一个Jspecies运行结果, 最后将所有结果保存在一个文件夹下。

(3)text_to_matrix.pl将多个平行运行Jspecies产生的结果文件转换成一个完整的ANIm矩阵文件;输入文件:文件夹存放有多个ANIm结果文件。

(4)ANIm_matrix_cluster.R根据“100-ANIm”进化距离值,对菌株进行聚类分析

 
 

Dr. Xiangyang Li (E-mail: lixiangyang@fudan.edu.cn, lixiangyang1984@gmail.com), Fudan university; Kaili University; Bacterial Genome Data mining & Bioinformatic Analysis (http://www.microbialgenomic.com/).

Copyright 2019, Xiangyang Li. All Rights Reserved.

   
 
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