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Recently, the deep sequence coverage generated by next-generation sequencing technologies has caused the amount of sequence to be processed during a genome project to grow rapidly, and has rendered current k-mer counting tools too slow and memory intensive. At the same time, large multicore computers have become commonplace in research facilities allowing for a new parallel computational paradigm. RESULTS: We propose a new k-mer counting algorithm and associated implementation, called Jellyfish, which is fast and memory efficient. It is based on a multithreaded, lock-free hash table optimized for counting k-mers up to 31 bases in length. Due to their flexibility, suffix arrays have been the data structure of choice for solving many string problems. For the task of k-mer counting, important in many biological applications, Jellyfish offers a much faster and more memory-efficient solution. AVAILABILITY: The Jellyfish software is written in C++ and is GPL licensed. 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A fast, lock-free approach for efficient parallel counting of occurrences of <i>k</i> -mers 论文

A fast, lock-free approach for efficient parallel counting of occurrences of <i>k</i> -mers · 相关技术

相关技术