目前组装软件常用的两种算法:overlap-layout-consensus (OLC)和de-bruijn-graph(DBG)。 OLC算法 OLC是一种直观算法(intuitionistic assembly algorithm),主要用于长的低丰度序列的组装,特别是一代和三代测序数据,常见的软件有Arachne、Celera Assembler、CAP3、PCAP、TIGR、AMOS、Phrap、Phusion和Newbler。其方法主要分为...
K-mer clustering algorithm using a MapReduce framework: application to the parallelization of the Inchworm module of TrinityMapReduceDe novo sequence assemblyRNA-SeqTrinityDe novo transcriptome assembly is an important technique for understanding gene expression in non-model organisms. Many de novo ...
124 软件技术·算法 Software Technique·Algorithm k-mer 变化范围(2~7)时, FTKC 和BTKC 的运行时间与 序列长度之间的关系. 从图中可以看出, 随着序列长 度的增加, 两种算法的运行时间也都呈线性增加. 该 观测结果也与我们在算法复杂度中的分析结果一致, 即两种算法的时间复杂度与序列长度的呈线性相关. ...
and then the ‘real’ parallel algorithm, involving multiple CPUs / cores and multiple disks (see Figure1). The algorithm description is valid for any parameterskand read lengthr. In fact, in the current implementationkcan be as large as 256, andras large as 10240, ...
andasupportvectormachine(SVM)algorithmtodistinguishlncRNAsfrommessengerRNAs(mRNAs),inthe absenceofgenomicsequencesorannotations.TheperformanceofPLEKwasevaluatedonwell-annotatedmRNA andlncRNAtranscripts.10-foldcross-validationtestsonhumanRefSeqmRNAsandGENCODElncRNAsindicated ...
Algorithm 1 Pseudocode of our method used to estimate proportions of sources in sink s Additionally, we performed a 5-fold cross-validation experiment by splitting the collection of metagenomic samples into 5 stratified folds with non-overlapping groups. The groups were defined by the BioProject from...
To improve the performance when not enough main memory is available to load the entire database into RAM, we added a new capability to KrakenUniq. When using this new feature, only a chunk of the database is loaded into memory at a time, after which the algorithm iterates over the reads...
K-mer clustering algorithm using a MapReduce approach Reduce的组装算法,通过统计去除组装过程中的错误数据,通过增加k-mer的长度消除组装过程中的重复数据,最后在Map Reduce平台实现了并行组装算法,实验结果表明算法提高了... SK Chang,MD Winn,V Sachdeva,... - Bioinformatics & Biomedicine 被引量: 0发表: ...
KTU: K-mer-based taxonomic clustering algorithm improves biological relevance in microbiome associated study - poyuliu/KTU
areD=4Kpossible words of lengthKin the DNA (RNA) alphabet, and in our study we tested word lengths from two to eight. The methods tested differ in the way they represent a sequence as K-mers and how this information is utilized in a statistical learning algorithm to achieve best possible...