Encyclopedia of Metagenomics

Living Edition
| Editors: Karen E. Nelson

FR-HIT Overview

Living reference work entry
DOI: https://doi.org/10.1007/978-1-4614-6418-1_222-3

Synonyms

Definition

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.

Introduction

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...

Keywords

Titanium 
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Copyright information

© Springer Science+Business Media New York 2014

Authors and Affiliations

  1. 1.Center for Research in Biological Systems (CRBS)University of California, San DiegoLa JollaUSA