A crucial step in metagenomic data analysis is fragment recruitment, a process of aligning sequencing reads to reference genomes. FR-HIT offers high speed and high sensitivity in recruiting large-scale metagenomic reads.
Microbiome data are directly obtained from various environments and contain genomics information of many known and novel microorganisms. An important step to study these organisms’ identity and abundance is to align the sequencing reads against the available reference genomes. This process was called fragment recruitment in the Global Ocean Sampling (GOS) project that surveyed the world’s oceans (Rusch et al. 2007).
A metagenomic dataset may have many novel species without available reference genomes. Even if references are available, the microbial species may undergo large variations. So a fragment recruitment method needs to...
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