近日,中国农业科学院饲料研究所屠焰/马涛团队在aBIOTECH 发表了题为“Impact of database choice and confidence score on the performance of taxonomic classification using Kraken2” 的研究论文,揭示了参考数据库和置信度选择对Kraken2物种...
--clean 清理Remove unneeded files from a built database --standard 下载标准库Download and build default database --help 帮助Print this message --version 版本信息Print version informationOptions: --db NAME 库位置Kraken 2 DB/library name (mandatory except for --help/--version) --threads # 线程...
kraken2可以自己构建数据库也可以下载构建好的数据库。 下载官方构建好的数据库(ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/),或者第三方构建好的数据库( https://github.com/rrwick/Metagenomics-Index-Correction) MiniKraken2_v1_8GB:(5.5GB)8GB Kraken 2 Database built from the refseq bacteria, arc...
This effect is particularly pronounced for smaller databases such as Minikraken and Standard-16, where no reads could be classified when the CS was above 0.4. In contrast, for larger databases such as Standard, nt and GTDB r202, precision and F1 scores improved significantly with increasing CS,...
～/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）
The tool most widely used for 16S rRNA analysis and classification today is the Quantitative Insights into Microbial Ecology (QIIME) software pack- age [21], which compares sequencing reads against a 16S rRNA reference database. The three standard 16S rRNA databases, each of which has somewhat ...
Standard Kraken Database: NCBI taxonomic information, the complete genomes in RefSeq for the bacterial, archaeal, and viral domains. 所以可以看到标准的库下载的是细菌、古菌以及病毒的RefSeq数据。 但是实际上我们知道,就人体微生物组数据而言,其实真菌也是很重要的组成部分,因此我们可以自主添加真菌数据库。
between0and1).--fast-buildDonot require database to be deterministically built when using multiple threads.Thisisfaster,but does introduce variabilityinminimizer/LCApairs.Usedwith--build and--standard options. 首先构建一个标准数据库看看吧,执行如下命令。
用kraken2-build命令创建时需要安装标记低复杂度区域的 dustmasker 工具,如果没有用--no-masking取消标记,否则工具会出错。创建标准的数据库直接用--standard命令,这将下载 NCBI 分类数据库,包含细菌、古细菌、病毒、人类和一些已知质粒载体。 kraken2-build --standard --threads 12 --no-masking --db ${db_dir...
--clean 清理Remove unneeded files from a built database --standard 下载标准库Download and build default database --help 帮助Print this message --version 版本信息Print version information Options: --db NAME 库位置Kraken 2 DB/library name (mandatory except for ...