8.8.5. Databases for metagenomics

Several sites have emerged for mapping metagenomic sequence reads and amplicons, including the longstanding Ribosomal Database Project for bacterial and archael 16S alignments (http://rdp.cme.msu.edu/), the SILVA databases for rRNA’s generally (http://www.arb-silva.de/), and MEGAN (ab.inf.uni-tuebingen.de/software/megan/), which aspires to map to targets across the tree of life. Each site allows for limited web searching, and for downloading relevant databases for more efficient local searches.