CAFE: aCcelerated Alignment-FrEe sequence analysis

Abstract

Alignment-free genome and metagenome comparisons are increasingly important with the development of next generation sequencing (NGS) technologies. Recently developed state-of-the-art k-mer based alignment-free dissimilarity measures including CVTree, \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$d_2^*$\end{document} and \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{upgreek} \usepackage{mathrsfs} \setlength{\oddsidemargin}{-69pt} \begin{document} }{}$d_2^S$\end{document} are more computationally expensive than measures based solely on the k-mer frequencies. Here, we report a standalone software, aCcelerated Alignment-FrEe sequence analysis (CAFE), for efficient calculation of 28 alignment-free dissimilarity measures. CAFE allows for both assembled genome sequences and unassembled NGS shotgun reads as input, and wraps the output in a standard PHYLIP format. In downstream analyses, CAFE can also be used to visualize the pairwise dissimilarity measures, including dendrograms, heatmap, principal coordinate analysis and network display. CAFE serves as a general k-mer based alignment-free analysis platform for studying the relationships among genomes and metagenomes, and is freely available at https://github.com/younglululu/CAFE.

Benchmarking of alignment-free sequence comparison methods

“…Availability AAF [72] exact k-mer count 10/01/201 7 https://github.com/fanhuan/AAF AFKS [32] 1.0 https://github.com/TulsaBioinformaticsToolsmith/ Alignment-Free-Kmer-Statistics alfpy [3] 1.0.6 https://github.com/aziele/alfpy CAFÉ [34] 1.0.0 https://github.com/younglululu/CAFE FFP [33,38] 2v.2.1 https://github.com/jaejinchoi/FFP jD2Stat [35] 1.0 http://bioinformatics.org.au/tools/jD2Stat/ LZW-Kernel [79] information theory NA https://github.com/kfattila/LZW-Kernel spaced [84][85][86] inexact k-mer count 1.0 http://spaced.gobics.de kWIP [78] k-mer count 0. Detailed information about the tools parameter values used in this study for different reference data sets is provided in Additional file: Table 1.…”

“…Currently, the most widely used AF approaches are based on k-mer counts [32]. These methods are very diverse, providing a variety of statistical measures that are implemented across different software tools [3,[33][34][35] (Table 1). Many k-mer methods work by projecting each of the input sequences into a feature space of k-mer counts, where sequence information is transformed into numerical values (e.g., k-mer frequencies) that can be used to calculate distances between all possible sequence pairs in a given data set.…”

The number of spaced-word matches between twoDNAsequences as a function of the underlying pattern weight

“…In the last few years, a number of alignment-free approaches have been proposed that are able to use unassembled short sequencing reads as input [54,14,39,33,3,47], as a basis for sequence clustering [1], for phylogenetic tree reconstruction [? ] or for phylogenetic placement [3].…”

Deformity Index: A semi-reference quality metric of phylogenetic trees based on their clades

“…The discrepancies between these two trees are shown in Red colored clade. [59] 3.90 15.92 Canberra [26] 3.54 4.71 Chebyshev [26] 15.03 37.31 Chi Square [26] 17.84 21.90 Co-Phylog [60] 4.24 4.84 Cosine [26] 4.06 10.33 CV Tree [38,63] 4.81 0.13 D * 2 [40,57] 3.34 11.01 Euclidean distance [26] 10. 26 19.38 FFP [46,47] 24.01 26.50 Fast Vector [25] 11.64 5.29…”