COGNIZER: metagenome 功能注释框架

标题：

COGNIZER: A Framework for Functional Annotation of Metagenomic Datasets

摘要：

Recent advances in sequencing technologies have resulted in an unprecedented increase in the number of metagenomes that are being sequenced world-wide. Given their volume, functional annotation of metagenomic sequence datasets requires specialized computational tools/techniques. In spite of having high accuracy, existing stand-alone functional annotation tools necessitate end-users to perform compute-intensive homology searches of metagenomic datasets against “multiple” databases prior to functional analysis. Although, web-based functional annotation servers address to some extent the problem of availability of compute resources, uploading and analyzing huge volumes of sequence data on a shared public web-service has its own set of limitations. In this study, we present COGNIZER, a comprehensive stand-alone annotation framework which enables end-users to functionally annotate sequences constituting metagenomic datasets. The COGNIZER framework provides multiple workflow options. A subset of these options employs a novel directed-search strategy which helps in reducing the overall compute requirements for end-users. The COGNIZER framework includes a cross-mapping database that enables end-users to simultaneously derive/infer KEGG, Pfam, GO, and SEED subsystem information from the COG annotations.

地址：

http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0142102

源码：

http://metagenomics.atc.tcs.com/function/cognizer/

安装：

wget http://metagenomics.atc.tcs.com/cognizer/application/COGNIZER_source_code.zip
unzip COGNIZER_source_code.zip
mv  source_code   cognizer-0.9b
cd cognizer-0.9b
gcc -O2 -g  cognizer.c  -o  cognizer

修改：为了方便在任何目录访问cognizer程序，需要修改源代码中的 blastall或者RAPSearch的路径模式，去掉相对路径，修改成只要环境变量可以访问RAPSearch 或者 blastall 就可以使用模式。
修改：数据库db相对路径修改成绝对路径，保证任何目录都可以访问。
修改：RAPSearch模式变成RAPSearch2 命令行接口模式， 多线程使用 -z ， 添加 bitscore 限制， 最小 bitscore 60；

导读：

COGNIZER 快速注释模式，采用了NCBI COG 数据库 ftp://ftp.ncbi.nih.gov/pub/COG/COG/myva 作为RAPSearch的库索引进行序列相似性比对，然后与其他数据库进行关联，比如GO、KEGG 、Fig等，最大的问题可能就是库比较小， MOCAT2: a metagenomic assembly, annotation and profiling framework 文章也提及COG谱要比COGNIZER好点，原因可能就是库上，另外COG注释的一个数据库是 eggNOG， 库还是比较大，不过使用diamond软件，速度应该和 myva+RAPSearch相当， 但是二者肯定比使用 blastall 作为序列比对引擎快， 如果能认可使用 NCBI 的COG 序列库进行序列相似性搜索，COGNIZER 还是很不错。

版本：

2016-12-01.v1