Aides the acquisition, storage, analysis and publication of DNA barcode records. BOLD is a cloud-based data storage and analysis platform which consists of four main modules: a data portal, an educational portal, a registry of BINs (putative species), and a data collection and analysis workbench. The software is a repository for the specimen and sequence records that form the basic data unit of all barcode studies, a workbench that aids the management, quality assurance and analysis of barcode data and also provides a vehicle for collaboration across geographically dispersed research communities.
Facilitates the design, optimization, and tracking of barcoded oligonucleotides. XSTK is useful for projects that require highly multiplexed polymerase chain reaction (PCR) and DNA sequencing. It builds a list of all possible DNA sequences of a specified length and then progressively culls sequences that may interfere with primary PCR amplification and/or sequencing steps.
A series of bioinformatics tools for high-throughput sequencing analysis, including pre-processing, clustering, database matching, and classification. With PANGEA, sequences obtained directly from the sequencer can be processed quickly to provide the files needed for sequence identification by BLAST and for comparison of microbial communities.
Creates DNA barcode sets capable of correcting insertion, deletion, and substitution errors. DNABarcodes generates sets from a few basic input parameters (e.g. length, distance metric, minimum distance, chemical properties). It satisfies the specifics of most particular experimental demands in de novo design of barcodes. Additionally, the package allows analysing existing sets of DNA barcodes as well as the generation of subsets of those existing sets to improve their error correction and detection properties. Finally, reads that start with a (possibly mutated) barcode can be demultiplexed, i.e., assigned to their original reference barcode. DNABarcodes was designed for speed, versatility, provable correctness and large set sizes.
Exploits taxon specific barcode sequences created through the BarcodeGenerator software to align metagenome reads. Barcoding is a command line application which uses BLASTN to align reads against the generated barcode sequences and then compute multiple settings to score results alignments and individual barcodes. This application can be used with both Roche and Illumina data.
Permits users to identify and estimate abundance of variants in a virus metapopulation. MetaGaAP generates a custom database from sequence data and comparison with ultra-deep sequencing of amplicons of novel, polymorphism-rich ‘barcode’ regions in the viral metagenome. It can be used in analysis of community composition where suitable reference sequence databases are not available, complete or accurately assigned, and can also be used to identify and quantify strain variants in pathology, ecology and evolutionary studies without the need for viral cloning.
Retrieves species thanks to the utilization of DNA barcoding or metabarcoding. FuzzyID is based on a Hidden Markov Model (HMM) algorithm to reduce the searching scope to genus level. It proceeds to identification of species employing minimum genetic distance. This tool provides an efficient and accurate species recognition protocol for biodiversity related projects with large DNA sequence datasets.