Reconstruction of 1,979 prokaryotic metagenome-assembled genomes from 37 global cave environments

This record contains a non-redundant catalog of cave metagenome-assembled genomes (MAGs) reconstructed from 37 caves with all companion tables needed for reuse. Representative genomes are given in two archives split by MIMAG quality; the full set of refined (pre-dereplication) MAGs is provided separately. Summary tables (Excel) cover sample metadata, genome quality, taxonomy, biosynthetic gene clusters (BGCs), antimicrobial-resistance genes (ARGs), functional annotations, and read-recruitment. Two HTML reports document the read quality before and after trimming.Root levelmetadata.xlsx — Sample metadata and sequencing statistics. Each row is a metagenome sample with accessions and context.MAGs_HQ.tar and MAGs_MQ.tar — 1,979 species-level representative MAGs split by qualitymagscot.tar — 4,234 refined MAGs retained from 25,276 candidate bins after bin refinement across three binners.HQ (high quality): ≥90% completeness and ≤5% contamination.MQ (medium quality): ≥50% completeness and ≤10% contamination.All MAG FASTA files are named: [RUN_ACCESSION]_cleanbin_[BIN_ID].faMAGs present in MAGs_HQ/MQ.tar are species-level representatives; MAGs found only in magscot.tar are non-representative refined MAGs.Unpacking archives.tar.zst: Decompress and then untar — Linux/macOS: tar -I unzstd -xf(or zstd -d&& tar -xf); Windows: open with 7-Zip (extract once to get the .tar, then extract the .tar to get the final folder).FoldersQCreport/Two interactive MultiQC HTML reports summarizing read quality:Report_BeforeQC.html — before trimmingReport_AfterQC.html — after trimmingOpen directly in a browser to view adapter content, base-quality profiles, etc.Analysis/The Excel workbooks provide all annotations needed to reuse the catalog.Every table is keyed by MAG_ID, to match the FASTA filename stem in the archives ([RUN_ACCESSION]_cleanbin_[BIN_ID].fa; e.g., ERR10479404_cleanbin_000031), so columns using MAG_ID map directly to the corresponding genome files.CheckM2.xlsx — Genome quality for all 4,234 draft MAGs (located in magscot.tar)Classification.xlsx — GTDB-Tk taxonomy classification for the representatives MAGsBGC.xlsx — antiSMASH 8.0 biosynthetic gene clusters output for the representatives MAGsARG.xlsx — DRAMMA ARG predictions for the representative MAGsDRAM.xlsx — DRAM functional annotation for the representative MAGsCoverM.xlsx — Read-recruitment of each sample against each representative MAGs本数据集包含一套非冗余的洞穴宏基因组组装基因组（metagenome-assembled genomes, MAGs）目录，其重构自37处洞穴样本，同时附带所有可复用所需的配套表格。代表性基因组分为两个归档文件，按MIMAG质量等级划分；全套经过精修（去重复前）的MAGs则单独提供。 汇总表格（Excel格式）涵盖样本元数据、基因组质量、分类学信息、生物合成基因簇（biosynthetic gene clusters, BGCs）、抗微生物耐药基因（antimicrobial-resistance genes, ARGs）、功能注释以及读段招募结果。另有两份HTML报告分别展示修剪前后的读段质量情况。 "Root_levelmetadata.xlsx"：样本元数据与测序统计信息，每一行对应一个宏基因组样本，包含登录号与背景信息。 "MAGs_HQ.tar"与"MAGs_MQ.tar"：包含1979个物种级代表性MAGs，按质量等级划分： - HQ（高质量）：完整度≥90%且污染率≤5%； - MQ（中等质量）：完整度≥50%且污染率≤10%。 "magscot.tar"：经3款组装工具进行bin精修后，从25276个候选bin中保留的4234个精修后MAGs。 所有MAG的FASTA文件命名格式为：[RUN_ACCESSION]_cleanbin_[BIN_ID].fa。其中，"MAGs_HQ.tar"与"MAGs_MQ.tar"中包含的MAG为物种级代表性基因组；仅存在于"magscot.tar"中的MAG为非代表性精修MAG。 归档文件解压说明：.tar.zst格式的归档文件需先解压，再解tar——Linux/macOS系统可使用命令：tar -I unzstd -xf（或zstd -d && tar -xf）；Windows系统可使用7-Zip打开（先解压一次得到.tar文件，再解压该.tar文件以获取最终文件夹）。 "QCreport/"文件夹：包含两份交互式MultiQC HTML报告，用于汇总读段质量： - "Report_BeforeQC.html"：修剪前的读段质量报告； - "Report_AfterQC.html"：修剪后的读段质量报告。 可直接在浏览器中打开查看接头序列、碱基质量分布等信息。 "Analysis/"文件夹内的Excel工作簿包含复用该目录所需的全部注释信息：所有表格均以"MAG_ID"作为键值，可与归档文件中的FASTA文件名前缀（即[RUN_ACCESSION]_cleanbin_[BIN_ID].fa，例如ERR10479404_cleanbin_000031）匹配，因此使用"MAG_ID"的列可直接映射至对应的基因组文件。各表格详情如下： - "CheckM2.xlsx"：对应"magscot.tar"中全部4234个草稿MAG的基因组质量信息； - "Classification.xlsx"：代表性MAGs的GTDB-Tk分类学注释结果； - "BGC.xlsx"：代表性MAGs的antiSMASH 8.0生物合成基因簇分析输出结果； - "ARG.xlsx"：代表性MAGs的DRAMMA抗微生物耐药基因预测结果； - "DRAM.xlsx"：代表性MAGs的DRAM功能注释结果； - "CoverM.xlsx"：各样本针对各代表性MAG的读段招募结果。