CANGS provides two layers of analysis: the Sequence Processing Layer is the first step, in which trims the sequences (removal of PCR primers, adapter sequence and sample identifiers) and filters low quality sequences (sequences with Ns, singletons, and sequences with very low average quality score). This file allows the user to specify all parameters needed for the processing of the 454 sequences. As a preparation step for CANGS, the options file CANGSOptions.txt needs to be customized. The arrows illustrate the path of data flow. Schema for processing and analyzing 454 GS-FLX sequencesįigure 1 shows the way in which the CANGS utility processes 454-sequence data sets. ĬANGS has been developed for Mac OS X but it also works on Linux and any other Unix system. CANGS can be used to assign the taxonomic grouping based on similarity with sequences from the NCBI database. We developed CANGS - a flexible and user-friendly utility to trim sequences, filter low quality sequences, and produce input files for further downstream analyses. This increase in the amount of sequence data requires efficient software tools for processing the raw data generated by next generation sequencers. PCR amplicons of more than 400 bp can be sequenced in a massively parallel manner which allows building a fine-grained catalog of species abundance patterns in a broad range of habitats. In addition to genome sequencing and transcriptome profiling, ultra-deep sequencing of short amplicons offers an enormous potential in clinical studies and in studies of ecological diversity. Next generation sequencing technologies have dramatically increased the sequence output at a substantially reduced cost. CANGS is written in Perl and runs on Mac OS X/Linux and is available at ConclusionĬANGS performs PCR primer clipping, filtering of low quality sequences, links sequences to NCBI taxonomy and provides input files for common rarefaction analysis software programs. 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. 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. The downstream analyses rely either on third party software (e.g.: rarefaction analyses) or CANGS-specific scripts. CANGS filters low quality sequences, removes PCR primers, filters singletons, identifies barcodes, and generates input files for downstream analyses. ![]() We developed CANGS ( C leaning and A nalyzing N ext G eneration S equences) a flexible and user-friendly integrated software utility: CANGS is designed for amplicon based biodiversity surveys using the 454 sequencing platform. A user-friendly software utility that carries out these steps is still lacking. In order to use NGS for biodiversity surveys, software tools are required, which perform quality control, trimming of the sequence reads, removal of PCR primers, and generation of input files for downstream analyses. In addition to the use in whole genome sequencing, the 454 GS-FLX platform is becoming a widely used tool for biodiversity surveys based on amplicon sequencing. Next generation sequencing (NGS) technologies have substantially increased the sequence output while the costs were dramatically reduced.
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