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metacrast website  

MetaCRAST (Metagenomic CRISPR Reference-Aided Search Tool) is a tool to detect CRISPR arrays in raw, unassembled metagenomes. Unlike other tools, it uses expected CRISPR direct repeat (DR) sequences from assembled contigs or bacterial genomes to guide metagenomic CRISPR detection. It uses a fast implementation of the Wu-Manber multipattern search algorithm to rapidly select reads that contain an expected DR sequence. It then proceeds through reads identified in the previous step to find DR sequences within acceptable distances of each other (i.e., with acceptable length spacers between them). Spacers between these DRs are then extracted and clustered into a non-redundant set with CD-HIT.

Environment Modules

Run module spider metacrast to find out what environment modules are available for this application.

System Variables

  • HPC_METACRAST_DIR - installation directory
  • HPC_METACRAST_BINMC - executable directory
  • HPC_METACRAST_BIN - executable directory
  • HPC_METACRAST_DAT - data directory
  • HPC_METACRAST_QUR - query directory


If you publish research that uses metacrast you have to cite it as follows:

If you use MetaCRAST in published work, please include a reference to my PeerJ article: Moller AG, Liang C. (2017) MetaCRAST: reference-guided extraction of CRISPR spacers from unassembled metagenomes.