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Crass specifications


Unique identifier OMICS_09627
Name Crass
Alternative name CRISPR Assembler
Software type Package/Module
Interface Command line interface
Restrictions to use None
Output data Crass outputs a standard xml file that describes all of the CRISPRs that it discovers. This file format is open source and is being developed to facilitate the interchange of CRISPR data between different research groups.
Operating system Unix/Linux
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes


No version available



  • person_outline Gene W. Tyson

Publication for CRISPR Assembler

Crass citations


Determining virus host interactions and glycerol metabolism profiles in geographically diverse solar salterns with metagenomics

PMCID: 5228507
PMID: 28097058
DOI: 10.7717/peerj.2844

[…] We detected CRISPR arrays in metagenomes using both de novo and reference-guided methods. We used Crass for de novo detection () and a custom pipeline (MetaCRAST) for reference-guided detection (see Materials and Methods). We used a combination of Halobacteriales and Haloferacales CRISPR direct re […]


MetaCRAST: reference guided extraction of CRISPR spacers from unassembled metagenomes

PMCID: 5592083
PMID: 28894651
DOI: 10.7717/peerj.3788
call_split See protocol

[…] , or 300) -md poly4 3e−3 3.3e−8. All Illumina read length distributions were uniform with all reads having exactly the average read length.Simulated metagenomes were searched for CRISPR spacers using Crass (), MinCED (Skennerton), and MetaCRAST. Crass and MinCED were run with default parameters (crass grinder-reads.fa; minced -spacers grinder-reads.fa minced.crispr). The default minimum and maximu […]


New CRISPR Cas systems from uncultivated microbes

PMCID: 5300952
PMID: 28005056
DOI: 10.1038/nature21059

[…] erformed using Phyre2. The HMM database, including the newly discovered Cas proteins, is available in Supplementary Data 6.Spacer sequences were determined from the assembled data using CrisprFinder. CRASS was used to locate additional spacers in short DNA reads of the relevant samples. Spacer targets (protospacers) were then identified by BLAST searches (using “-task blastn-short”) against the re […]


Ultrastructure and Viral Metagenome of Bacteriophages from an Anaerobic Methane Oxidizing Methylomirabilis Bioreactor Enrichment Culture

Front Microbiol
PMCID: 5099504
PMID: 27877158
DOI: 10.3389/fmicb.2016.01740

[…] et al., ), and the total bitscore for each viral contig was recorded. Second, both Methylomirabilis genomes were checked for CRISPR sequences using CRISPRfinder ( and CRASS (Skennerton et al., ). The resulting spacer sequences were subsequently cross-referenced with the viral genomes and contigs from the SPAdes assembly using CRISPRtarget (Biswas et al., ). Third, […]


Metagenomic Analysis of Bacterial Communities of Antarctic Surface Snow

Front Microbiol
PMCID: 4814470
PMID: 27064693
DOI: 10.3389/fmicb.2016.00398
call_split See protocol

[…] To construct a set of CRISPR arrays for each metagenomic dataset we used CRASS algorithm (Skennerton et al., ) with default parameters: repeat lengths 23–47 bp, spacer lengths 26–50 bp, and minimum three spacers in array as default parameters. Spacer and repeat sequences w […]


A modular toolbox for gRNA–Cas9 genome engineering in plants based on the GoldenBraid standard

Plant Methods
PMCID: 4736081
PMID: 26839579
DOI: 10.1186/s13007-016-0101-2

[…] ters are available in the GB collection) and with the scaffold RNA in a cyclic digestion/ligation Golden Gate reaction [] to build the complete gRNA expression cassette. This step is assisted by the ‘CRISPR Assembler’ tool available at 1The conditions for gRNA assembly were optimized by checking three key parameters, namely primer concentration, […]


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Crass institution(s)
Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences; Advanced Water Management Centre, The University of Queensland, St Lucia, Brisbane, Queensland, Australia

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