例如,Web of Life ( WoL ) 和Genome Taxonomy Database ( GTDB ) 提供的全基因组树只覆盖了一小部分已知的细菌和古细菌,而SILVA和Greengenes则较为全面,但通常无法链接到基因组。 本研究作者利用迭代的方法产生一个单一的大规模参考树,统一这些不同的数据层(基因组和16S rRNA),即为Greengenes2。数据来源及主要...
例如,Web of Life ( WoL ) 和Genome Taxonomy Database ( GTDB ) 提供的全基因组树只覆盖了一小部分已知的细菌和古细菌,而SILVA和Greengenes则较为全面,但通常无法链接到基因组。 本研究作者利用迭代的方法产生一个单一的大规模参考树,统一这些不同的数据层(基因组和16S rRNA),即为Greengenes2。数据来源及主要...
The reference database release contains the following artifacts. <version> refers to the version of the database, which follows a YYYY.MM format. The feature IDs present in the artifacts use the WoL namespace for genomes. For ASVs, we provide reference files which use the ASV, MD5 hashes,...
(ref.9; samples selected and sequenced specifically for Greengenes2) were collected and deduplicated. Sequences were then aligned using UPP25, and gappy sequences with less than 1,000 base pairs were removed. The resulting set of 321,210 unique sequences was used with uDance v1.1.0 to ...
using gg_13_8_train_ids_97.fasta.gz in assignTaxonomy will assign the OTUID along with the paired taxonomy so you don't have to add it back later. FYI this "third" database performs exactly the same as the rep_set/97_otus.fasta when using RDP since the IDs are now factored into ...
Running time of Parallel-META 1.0 and 2.0 with the same datasets and reference database (Greengenes).Xiaoquan SuWeihua PanBaoxing SongJian XuKang Ning
一个关键问题是全基因组资源和rRNA资源依赖于不同的分类和系统发育。例如,生命之网(Web of Life,WoL)和基因组分类数据库(Genome Taxonomy Database, GTDB)提供的全基因组树仅涵盖一小部分已知细菌和古细菌,而SILVA和Greengenes更全面,但通常无法链接到基因组。
造成这样结果的一个关键原因是二者依赖于不同的分类和系统发育。例如,Web of Life ( WoL ) 和Genome Taxonomy Database ( GTDB ) 提供的全基因组树只覆盖了一小部分已知的细菌和古细菌,而SILVA和Greengenes则较为全面,但通常无法链接到基因组。 本研究作者利用迭代的方法产生一个单一的大规模参考树,统一这些不同...
The reference database release contains the following artifacts. <version> refers to the version of the database, which follows a YYYY.MM format. The feature IDs present in the artifacts use the WoL namespace for genomes. For ASVs, we provide reference files which use the ASV, MD5 hashes,...