Article - MPS-Sampling

All the data about the article of MPS-Sampling.
MPS-Samping (data of the analysis from MPS-Sampling)ADB (Artificial genomes generated from RiboDB data)datafasta.tar.gz (a file to unzip, containing all the protein sequences from GTDB)genome_index (the index csv file used by MPS-Sampling)SamplesSample_X (a directory for each tested sample)inputgenome_index (the index csv file used by MPS-Sampling)output4.MPS_results_directorye_value_1e-05_cov_mode_0_min_cov_0.8_min_seq_id_0.6delta_0.4MPS_links.csv (A file with two columns, containing the link between each original genome (first column) and its MPS-representative (second column).)MPS_representatives.csv (A file with one column, contain the MPS-representatives chosen by MPS-Sampling.)GTDB (Genome-Based Database)inputfasta.tar.gz (a file to unzip, containing all the protein sequences from GTDB)genome_index.csv (the index csv file used by MPS-Sampling)output4.MPS_results_directorye_value_1e-05_cov_mode_0_min_cov_0.8_min_seq_id_0.6delta_X (There is a directory for each delta from {0.05, 0.1, ... , 0.95, 1}.)MPS_links.csv (A file with two columns, containing the link between each original genome (first column) and its MPS-representative (second column).)MPS_representatives.csv (A file with one column, contain the MPS-representatives chosen by MPS-Sampling.)RiboDB (Ribosomal Database)inputfasta.tar.gz (a file to unzip, containing all the protein sequences from RiboDB, after filtering)genome_index.csv (the index csv file used by MPS-Sampling)output4.MPS_results_directorye_value_1e-05_cov_mode_0_min_cov_0.8_min_seq_id_0.6delta_X (There is a directory for each delta from {0.05, 0.1, ... , 0.95, 1}.)MPS_links.csv (A file with two columns, containing the link between each original genome (first column) and its MPS-representative (second column).)MPS_representatives.csv (A file with one column, contain the MPS-representatives chosen by MPS-Sampling.)phylogeny (data about the phylogenetic inference)Bacillaceaeconcat_cleaned.fst (the supermatrix used for the phylogenetic inference)FastTree_iTOL.nw (the inferred phylogeny, as it was used on iTOL)Bacterial backboneconcat_cleaned.fst (the supermatrix used for the phylogenetic inference)FastTree_iTOL.nw (the inferred phylogeny, as it was used on iTOL)Enterobacteriaceaeconcat_cleaned.fst (the supermatrix used for the phylogenetic inference)FastTree_iTOL.nw (the inferred phylogeny, as it was used on iTOL)Lactobacillaceaeconcat_cleaned.fst (the supermatrix used for the phylogenetic inference)FastTree_iTOL.nw (the inferred phylogeny, as it was used on iTOL)

本数据集涵盖所有与MPS-Sampling相关的研究文章数据。
MPS-Samping（MPS-Sampling）：源自MPS-Sampling的分析数据
ADB：基于RiboDB数据生成的人工基因组
datafasta.tar.gz：可解压文件，内含GTDB（Genome-Based Database，基因组数据库）的全部蛋白质序列
genome_index：MPS-Sampling使用的索引CSV文件
Samples：包含各待测样本对应的目录Sample_X
Sample_X内的文件结构：
input：genome_index（MPS-Sampling使用的索引CSV文件）
output：4.MPS_results_directory
该目录下包含参数配置为e_value_1e-05_cov_mode_0_min_cov_0.8_min_seq_id_0.6的子目录delta_0.4
MPS_links.csv：该文件包含两列数据，记录每个原始基因组（第一列）与其MPS代表序列（第二列）之间的对应关系
MPS_representatives.csv：该文件仅包含一列数据，内含MPS-Sampling筛选得到的MPS代表序列

GTDB（Genome-Based Database，基因组数据库）相关数据：
input：datafasta.tar.gz（可解压文件，内含GTDB的全部蛋白质序列）、genome_index.csv（MPS-Sampling使用的索引CSV文件）
output：4.MPS_results_directory
该目录下包含参数配置为e_value_1e-05_cov_mode_0_min_cov_0.8_min_seq_id_0.6的子目录delta_X，其中delta_X对应取值为{0.05, 0.1, ..., 0.95, 1}的每个delta值均单独对应一个目录
MPS_links.csv：该文件包含两列数据，记录每个原始基因组（第一列）与其MPS代表序列（第二列）之间的对应关系
MPS_representatives.csv：该文件仅包含一列数据，内含MPS-Sampling筛选得到的MPS代表序列

RiboDB（Ribosomal Database，核糖体数据库）相关数据：
input：datafasta.tar.gz（可解压文件，内含经过过滤的RiboDB全部蛋白质序列）、genome_index.csv（MPS-Sampling使用的索引CSV文件）
output：4.MPS_results_directory
该目录下包含参数配置为e_value_1e-05_cov_mode_0_min_cov_0.8_min_seq_id_0.6的子目录delta_X，其中delta_X对应取值为{0.05, 0.1, ..., 0.95, 1}的每个delta值均单独对应一个目录
MPS_links.csv：该文件包含两列数据，记录每个原始基因组（第一列）与其MPS代表序列（第二列）之间的对应关系
MPS_representatives.csv：该文件仅包含一列数据，内含MPS-Sampling筛选得到的MPS代表序列

phylogeny（系统发育推断相关数据）：
Bacillaceae：
concat_cleaned.fst：用于系统发育推断的超级矩阵文件
FastTree_iTOL.nw：用于iTOL平台的推断系统发育树文件
Bacterial backbone：
concat_cleaned.fst：用于系统发育推断的超级矩阵文件
FastTree_iTOL.nw：用于iTOL平台的推断系统发育树文件
Enterobacteriaceae：
concat_cleaned.fst：用于系统发育推断的超级矩阵文件
FastTree_iTOL.nw：用于iTOL平台的推断系统发育树文件
Lactobacillaceae：
concat_cleaned.fst：用于系统发育推断的超级矩阵文件
FastTree_iTOL.nw：用于iTOL平台的推断系统发育树文件