G. Alexeev, Assessment of k-mer spectrum applicability for metage- nomic dissimilarity analysis, BMC Bioinformatics 17 (1) (2016) 38. doi:10.1186/s12859-015-0875-7. URL http://dx.doi.org/10.1186/s12859-015-0875-7http: //www.biomedcentral.com/1471-2105/17/38...
The k-mer spectrum of this read set can be used for independently evaluating assembly quality without the need of a high quality reference. Merqury provides a set of tools for this purpose.Dependencygcc 10.2.0 or higher (for installing Meryl) Meryl v1.4.1 Java run time environment (JRE) ...
The choice of k-mer length of 25 nt is an optimal size for human-sized genomes which was used in ALLPATHS-LG for analyzing k-mer abundance spectrum49. K-mer based methods are independent of read mapping that typically relies on a reference sequence. Therefore they allow the establishment ...
Yak is initially developed for two specific use cases: 1) to robustly estimate the base accuracy of CCS reads and assembly contigs, and 2) to investigate the systematic error rate of CCS reads. It achieves the goals by comparing sequences to the k-mer spectrum of short reads or by compari...
Liu Y, Schröder J, Schmidt B: Musket: a multistage k-mer spectrum-based error corrector for Illumina sequence data. Bioinformatics. 2013, 29: 308-315. Article PubMed CAS Google Scholar Li X, Waterman MS: Estimating the repeat structure and length of DNA sequences using l-tuples. Genom...
strings (forward, reverse-complemented, or both) and no otherk-mer. We denote such a set as aspectrum preserving string set(SPSS). Note that this definition is different from the SPSS defined by Rahman and Medvedev [44], who consider an SPSS to include the additional restriction that each...
contained in sequencing reads. The impact of sequencing errors could be alleviated by error correction of sequences. The choice of k-mer length of 25 nt is an optimal size for human-sized genomes which was used in ALLPATHS-LG for analyzing k-mer abundance spectrum49....
The KTU R-package was built with additional functions for evaluating re-clustering efficacies and for assigning taxonomies based on the K-mer frequency spectrum and cosine dissimilarity. The full description is shown in the Supporting Information. 3 CASE STUDIES 3.1 Methods To verify that the KTU ...
k-mer:在生物信息学中,k-mers是包含在生物序列中的长度为k的子序列。 比如序列:GTAGAGCTGT,根据k值不同,可得到以下k-mer。 注:长度为L的序列对于一个给定的K可以得到L-k+1个k-mers。 file 2.可视化k-mers---k-mer spectrum k-mer spectrum:显示了序列中的每个k-mer的多重性(例:8-mers' frequency...
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