Anvi’o: an advanced analysis and visualization platform for ‘omics data. PeerJ. 2015;3:e1319. Article PubMed PubMed Central Google Scholar Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357–9. Article CAS PubMed PubMed Central Google Scholar ...
Anvi’o: an advanced analysis and visualization platform for ‘omics data. PeerJ. 2015;3:e1319. Article PubMed PubMed Central Google Scholar Langmead B, Salzberg SL. Fast gapped-read alignment with Bowtie 2. Nat Methods. 2012;9:357–9. Article CAS PubMed PubMed Central Google Scholar ...
(NCBI GRCm38) for normal mouse samples, or a pseudo-genome that combined reference human and mouse genomes for PDX samples, using Bowtie2 software79; PCR duplications (i.e., reads with identical ending positions) were identified and removed using in-house programs, and ...
虽然Bowtie2、SOAP2和BWA都采用了BWT算法,然而三种软件还有差别。其中Bowtie2采用Ferragina 和Manzini 提出的FM (Full-text minute-space)-index算法,为基因组序列创建具有后缀矩阵特性的 FM 索引数据结构,实现短序列的快速搜索;SOAP2则采用的是 BWT 算法压缩基因组序列哈希表索引数据结构进行精确匹配,采用“分割短序...
tool_pathPath to a directory containing all the need external software, e.g. thetools.tar.gz picard_pathNeeded for sam to fastq conversion trim_galore_pathNeeded for read trimming cutadapt_pathNeeded for read trimming bowtie2_pathNeeded for all against all alignment (cluster finding) ...
Bowtie 2 http://bowtie-bio.sourceforge.net/bowtie2 序列比对工具,短读长序列快速比对至参考序列,结果为SAM/BAM格式 [68] MetaPhlAn2 https://bitbucket.org/biobakery/metaphlan2/ 物种组成定量流程,包括人工整理的上万物种中的上百万个标记基因数据库,结果可直接用于LEfSe分析 [47] HUMAnN2 https://bitbuc...
The open source software includes the following external tools: bcl2fastq v2.17.1.14, Trimmomatic v0.32, Bowtie v2.2.4 and BLAST v2.2.30. A description of all open source code is included in Methods and further details are available on request. The proprietary portions of the code are not...
analyzed using 130 nt + 21 nt paired-end sequencing on Illumina sequencers. Adapter sequences were removed from read 1 (130 nt), and UMI sequences were extracted from read 2 (21 nt). The processed read 1 sequences were then aligned to designed BDA amplicons using the Bowtie2 software38...
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Software and algorithms Samtools Li et al.12 http://samtools.sourceforge.net/ bowtie2 Langmead and Salzberg13 http://bowtie-bio.sourceforge.net/bowtie2/index.shtml scBS-map Wu et al.14 https://github.com/wupengomics/scBS-map bedtools Quinlan and Hall15 https://bedtools.readthedocs.io...