CANGS

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Application data

Created by Ram Vinay Pandey, Viola Nolte, and Christian Schlötterer
Biological application domain(s) Metagenomics, Phylogenetics
Principal bioinformatics method(s) Primer removal, Sequence trimming, Sequencing quality control
Technology 454
Maintained? Yes
Programming language(s) Perl
Interface type(s) Command line
Resource type(s) Command-line tool

Summary: CANGS is a flexible and user-friendly utility to trim sequences, filter low quality sequences, and produce input files for further downstream analyses for 454 sequences. CANGS can be used to assign the taxonomic grouping based on similarity with sequences from the NCBI database

We developed CANGS (Cleaning and Analyzing Next Generation Sequences) a flexible and user-friendly integrated software utility: CANGS is designed for amplicon based biodiversity surveys using the 454 sequencing platform. CANGS filters low quality sequences, removes PCR primers, filters singletons, identifies barcodes, and generates input files for downstream analyses. The downstream analyses rely either on third party software (e.g.: rarefaction analyses) or CANGS-specific scripts. The latter include modules linking 454 sequences with the name of the closest taxonomic reference retrieved from the NCBI database and the sequence divergence between them. Our software can be easily adapted to handle sequencing projects with different amplicon sizes, primer sequences, and quality thresholds, which makes this software especially useful for non-bioinformaticians.

CANGS performs PCR primer clipping, filtering of low quality sequences, links sequences to NCBI taxonomy and provides input files for common rarefaction analysis software programs. CANGS is written in Perl and runs on Mac OS X/Linux and is available at

Links


References

  1. Pandey RV, Nolte V, Schlötterer C.. 2010. BMC Res Notes


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