"nr", "nt", "env_nr", "env_nt", "UniVec", "UniVec_Core") --special TYPE 特殊数据库,包括3种Download and build a special database (TYPE = one of "greengenes", "silva", "rdp") --add-to-library FILE 添加文件到库中 Add FILE to library --build 建索引Create DB from library (re...
所以,在使用Kraken2进行物种注释时,建议使用更全面的参考数据库(standard、nt和GTDB数据库),并结合适度的置信度(0.2-0.4)来提高分类的准确性和灵敏度。 中国农业科学院饲料研究所博士研究生刘云龙为文章第一作者,屠焰研究员和马涛副研究员...
Because Kraken 2 only stores minimizers in its hash table, andkcan be much larger thanℓ, only a small percentage of the possibleℓ-mers in a genomic library are actually deposited in the database. This creates a situation similar to the Kraken 1 "MiniKraken" databases; however, prelimi...
kraken2可以下载如下:”archaea”, “bacteria”, “plasmid”, “viral”, “human”, “fungi”, “plant”, “protozoa”, “nr”, “nt”, “env_nr”, “env_nt”, “UniVec”, “UniVec_Core”数据库,也可以指定下载数据库: kraken2-build --download-library nr --threads 24 --db $DBNAME #...
In contrast, for larger databases such as Standard, nt and GTDB r202, precision and F1 scores improved significantly with increasing CS, highlighting their robustness to stringent conditions. Recovery rates were mostly stable, indicating consistent detection of species under different CS settings. ...
The other option is building an nt database to try and get the largest picture of what is in the database. Author luthientinuviel commented Apr 14, 2020 via email Thanks Jen. If anyone else is willing to share their experience with Kraken 2 in human gut microbiome, I would really ...
～/software/Bracken/bracken-build -d ~/dbminikraken2_v1_8GB -t 8 -k 35 -l 150 #结束后会在kraken数据库路径下⽣成database150mers.kmer_distrib Bracken参数解释：-d，Kraken数据库路径；-t，线程数；-k，k-mer长度，Kraken1默认为31，Kraken2默认为32；-l，reads读长。数据库下载（第⼆种）
nt: NCBI non-redundant nucleotide database #非冗余蛋白库 UniVec: NCBI-supplied database of vector, adapter, linker, and primer sequences that may be contaminating sequencing projects and/or assemblies #常用污染序列,如载体、头、引物等 UniVec_Core: A subset of UniVec chosen to minimize false posi...
现在有了nt数据库下面animal的序列,那么如何构建kraken2的数据库呢? 首先推荐把kraken2安装到单独的conda环境中,而不是把kraken2直接安装 conda install kraken2 #不推荐 这种虽然方便,但是很可能与其它软件产生环境变量冲突 看了看kraken2的说明书,它提供”archaea”, “bacteria”, “plasmid”, “viral”, “hum...
"nr", "nt", "env_nr", "env_nt", "UniVec", "UniVec_Core") --special TYPE 特殊数据库,包括3种Download and build a special database (TYPE = one of "greengenes", "silva", "rdp") --add-to-library FILE 添加文件到库中 Add FILE to library ...