EasyMetagenome v1.20 (2023.11)

Update logs:

1. MetaPhlAn4’s new species annotations are converted to GTDB and diversity calculation scripts

2. Integrate Prof. Chen Tong’s corrections using Pipeline

3. CoverM quantifies the relative abundance of MAGs, merges and averages the results, and adds them to the tree annotation results.

4. The conda package of drep is 3.4.2, which lacks checkm (267M) and is replaced by the old version 2.6.2 (526M).

5. The dbCAN3 database is updated to the 2023 version, and the new diamond version builds indexes faster

6. Kneaddata quality control is skipped, fastp quality control is a required step.

7. Upgrade mutliqc from 1.14 to 1.15

8. Added Chapter 5: Single bacterial genome analysis process

9. Updated the Kraken2 database to version 20231009, adding alpha, beta diversity, Krona web page, and Pavian Sankey diagram

10. Added optional checkm2 evaluation

11. MetaPhlAn4新增物种注释转换为GTDB、多样性计算脚本

12. 整合陈同老师用Pipeline的修正

13. CoverM定量MAGs相对丰度、结果合并和求均值，并添加到进入树注释结果中

14. drep的conda包为3.4.2缺少checkm(267M)，替换为旧版2.6.2(526M)

15. dbCAN3数据库更新为2023版，diamond新版建索引更快

16. Kneaddata质控跳过，fastp质控为必选步骤

17. mutliqc升级1.14为1.15

18. 增加第五章：单菌基因组分析流程

19. 更新Kraken2数据库为20231009版本，新增alpha, beta多样性、Krona网页、Pavian桑基图

20. 新增可选的checkm2评估

EasyMetagenome v1.19 (2023.7)

1.19 2023.7.13

1. HUMAnN2+MetaPhlAn2为3和4
2. Kraken2数据库不同版本统一官方名称，仍使用3月版本数据库，最新版6月数据库官方文件有不完整
3. GTDB-tk数据库更新为214版

EasyMetagenome v1.18 (2023.4)

1. Update all the software the database
2. Provide the software and database backup site in http://nmdc.cn/datadownload or https://pan.baidu.com/s/1Ikd_47HHODOqC3Rcx6eJ6Q?pwd=0315

EasyMetagenome v1.14 (2022.3)

1.14 2022.3.25

1. EasyMicrobiome升级为1.14
2. 升级miniconda2为miniconda3
3. dbcan2从2020/7/31的808M更新为2021/9/24版1016M，格式变化，配套format_dbcan2list.pl更新
4. 新增eggnog环境，包含emapper 2.1.6，summarizeAbundance.py含pandas (conda install sklearn-pandas)，配套更新数据库
5. rgi更新到最新版及配套代码

First release

v1.11

2021.5