kraken2-build --download-taxonomy --threads 24 --db $DBNAME for line in `ls /media/bio1/build_database/db/library/db` do ##这一步是将序列加入到要构建的数据库中,进行预处理 kraken2-build --add-to-library /media/bio1/build_database/db/library/db/$line --db $DBNAME done ##建库 k...
Hi, i am using kraken from a supercomputer using linux. When i try to download de database i get this error kraken2-build --standard --db kraken Downloading nucleotide gb accession to taxon map...rsync: [Receiver] failed to c onnect to f...
6、命令分析 kraken2 --db ~/database/minikraken2/minikraken_8GB_20200312 --threads 20 --report ./test.report --output ./test.output --paired ../SRR13188906_1.fastq ../SRR13188906_2.fastq 这是一个Kraken2的命令,用于对一组宏基因组测序数据进行物种注释。具体来说,该命令使用了一个名为"mini...
by increasing the value ofkwith respect toℓ(using the--kmer-lenand--minimizer-lenoptions tokraken2-build); and secondly, through downsampling of minimizers (from both the database and query sequences) using a hash function. This
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...
～/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）
Results Prior to classification, Kraken requires users to first build a specialized database consisting of three files: taxo.k2d, opts.k2d, and hash.k2d. The user also can choose the value k that determines the length of the sequences that Kraken uses for its index; every sequence (or ...
Kraken2将在该路径下创建一个名为<database>的数据库文件夹,并将数据库文件下载到其中。如果您已经下载了数据库文件,可以使用以下命令将其解压到<path/to/database>中: kraken2-build --uncompress <database> 验证数据库 下载完成后,您可以使用Kraken2提供的工具验证数据库文件的完整性。以下是验证数据库文件...
hits to the vector database #常用污染序列核心库 标准模式下建的数据库只包括archaea、bacteria、human、plasmid、UniVec_Core、viral。 可以给一个db库下载多个数据 kraken2-build --download-library archaea --db $DBNAME kraken2-build --download-library viral --db $DBNAME ...
--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 (requires taxonomy d/l'ed and at least one file ...