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Protocols

crAss specifications

Information


Unique identifier OMICS_07300
Name crAss
Alternative name Cross-Assembly of Metagenomes
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Publication for Cross-Assembly of Metagenomes

crAss citations

 (10)
call_split

Environmental drivers of viral community composition in Antarctic soils identified by viromics

2017
Microbiome
PMCID: 5518109
PMID: 28724405
DOI: 10.1186/s40168-017-0301-7
call_split See protocol

[…] ontig abundance profiles []. Briefly, post-QC reads of all 14 viromes were assembled together using CLC. The .ace file containing mapping information and individual read files were then analyzed with crAss version 2.0 []. […]

library_books

Metagenomic Approaches to Assess Bacteriophages in Various Environmental Niches

2017
Viruses
PMCID: 5490804
PMID: 28538703
DOI: 10.3390/v9060127

[…] er than phylogenetic markers) will more likely be assembled into large contigs []. Other reference-independent tools include MaxiPhi [], which analyses inter-sample diversity between two samples, and crAss [], which facilitates the simultaneous cross-assembly of all samples in a data set.These tools offer just a sample of those available, and the range of bioinformatic tools ready for use in the a […]

library_books

Pharmacometabolomics Informs Viromics toward Precision Medicine

2016
Front Pharmacol
PMCID: 5081366
PMID: 27833560
DOI: 10.3389/fphar.2016.00411

[…] tabases ().To assist viromics data analysis similarity-independent methods have been also developed. PHACCS assesses the biodiversity of uncultured viral communities and quantifies virotypes (; ) and CRASS allows the simultaneous cross-assembly of all the samples in a dataset to identify shared viruses (). MaxiPhi uses pairwise assemblies from pooled viromes (). To tackle chimeras, the overlap–lay […]

library_books

Metagenomic analysis of planktonic microbial consortia from a non tidal urban impacted segment of James River

2015
Stand Genomic Sci
PMCID: 4575436
PMID: 26388969
DOI: 10.1186/s40793-015-0062-5

[…] Whole-genome shotgun sequence data were compiled and assessed using three methods (MG-RAST, MEGAN, and crAss []). Bar charts of normalized counts of the highest representative taxa were constructed using the MG-RAST output with an e-value cutoff of 1e-5, 60 % identity, and a minimum alignment length of […]

library_books

From cultured to uncultured genome sequences: metagenomics and modeling microbial ecosystems

2015
PMCID: 4611022
PMID: 26254872
DOI: 10.1007/s00018-015-2004-1

[…] ment of new bioinformatic tools and methods for metagenomic analysis. We turn now to some significant examples of uncultured genome sequences that were obtained from recycled datasets.Cross-assembly (crAss) of different samples from similar environments is one example of a strategy that can point to co-occurring sequences that are shared between environments and may not be identified with other me […]

call_split

Biodiversity and distribution of polar freshwater DNA viruses

2015
Sci Adv
PMCID: 4640604
PMID: 26601189
DOI: 10.1126/sciadv.1400127
call_split See protocol

[…] x (using subsamples of 252,867 reads, 70 bp in length). To further study the relationships between the subsampled individual viromes, we followed the recently described reference-independent strategy crAss (). Briefly, all sequences were combined in a single pool and then assembled using idba_ud (see below) generating cross-contigs. Then, reads from each environment were mapped onto these cross-co […]

Citations

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crAss institution(s)
Centre for Molecular and Biomolecular Informatics, Nijmegen Centre for Molecular Life Sciences, Radboud University Medical Centre, Netherlands

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