Journal
NUCLEIC ACIDS RESEARCH
Volume 45, Issue W1, Pages W554-W559Publisher
OXFORD UNIV PRESS
DOI: 10.1093/nar/gkx351
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Funding
- NSF [DMS-1518001]
- OCE [1136818]
- NIH [R01GM12062 4]
- Gordon and Betty Moore Foundation Marine Microbiology Initiative [GBMF3779]
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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, d(2)* and d(2)(S) 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.
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