Metagenomics profiling of samples from ICU patients
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下载链接：
https://zenodo.org/record/10684407
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资源简介：
Datasets from "Loss of microbial diversity and pathogen domination of the gut microbiota in critically ill patients" by Ravi et al.
PMID: 31526447
PMCID: PMC6807385
DOI: 10.1099/mgen.0.000293
Have been profiled using Kraken2 (three different databases), SingleM, KMCP (GTDB database) and MetaPhlAn 4.
The output files are shared via this repository.
Input datasets
Sample
#Seq
Total bp
SRX5707173
1,981,484
251,334,383
SRX5707285
4,534,703
552,669,038
SRX5707290
63,972
6,961,885
SRX5707359
561,807
62,895,743
SRX5707366
23,921,451
2,832,669,901
SRX5707374
10,304,335
1,252,385,596
SRX5707377
10,580,411
1,279,917,137
Profilers used
Kraken2 2.1.0, using these databases
k2_nt_20230502
k2_standard_20230314
KMCP 0.9.4 (db v2023.05)
SingleM (default db: S3.2.1.GTDB_r214.metapackage_20231006.smpkg.zb)
MetaPhlAn 4 4.0.6 (default db)
Methodology
see https://github.com/quadram-institute-bioscience/datasciencegroup/wiki/Kraken2-dataset.md
创建时间：
2024-02-21
