Once denoising and additional quality control processes are completed, chimeric sequences should be removed from the dataset. Chimeras are artificial recombinants between two or more parental sequences, and they are normally formed when prematurely terminated fragments reanneal to other template DNA during PCR amplification.
Aims to be a comprehensive software package that allows users to use a single piece of software to analyze community sequence data. mothur builds upon previous tools to provide a flexible and powerful software package for analyzing sequencing data. Extensive community-supported documentation and support are available through a MediaWiki-based wiki and a discussion forum.
A package that detects chimeric sequences from PCR with two or more segments, avoiding to interpret them as novel species. UCHIME uses a database containing no chimera-sequences or detects chimeras de novo by exploiting abundance data. This software displays a better sensitivity than ChimeraSlayer, which was the previous most sensitive detection method.
Houses tools for researchers to process and analyze their own functional gene sequencing data. FGP offers a pipeline where researchers can assemble a set of analysis tools to process a nucleotide sequence file, filter chimeric sequences, translate the nucleotide sequences, align, and cluster the protein sequences and additionally run the optional cluster file analysis tools. FGP allows libraries of sequence reads to be analyzed through either reference-based or unsupervised approaches after common initial processing steps. Reference-based approaches, such as the FrameBot frameshift correction and nearest neighbor tool offered by FGP, require a set of representative sequences, which can be compiled using the FunGene Repository (FGR).
Aims to address a major challenge facing researchers today — namely, analyzing, transferring, and storing biomedical "big data" — through the use of cloud-based resources. Nephele is a project from the National Institutes of Health (NIH) that brings together microbiome data and analysis tools in a cloud computing environment. Nephele's advanced analysis pipelines include multiple stages of data processing, many of which can be configured by modifying parameters provided in the submission form.
Examines the sequence conservation between a query and a trusted reference sequence, both in NAST alignment format. WigeoN is a flexible command-line based reimplementation of the Pintail algorithm. WigeoN is useful for flagging chimeras and anomalies only in near full-length 16S rRNA sequences. Although WigeoN provided effective chimeric sequence detection with full-length sequences, it lacked sensitivity at shorter sequence lengths. WigeoN is part of the Microbiome Utilities package.