Allows users to perform post clustering curation of amplicon data. LULU is an open source package which intends to decrease erroneous operational taxonomic units (OTUs) in a targeted dataset. The software was developed with the aim of reducing taxonomic redundancy and improving community composition. It was applied on twenty different initial OTU definition approaches.
Facilitates baits’ designing and testing for hybridization capture. BaitsTools generates high-quality oligonucleotide baits from a wide range of formats from reference sequences or across the break in linearized circular sequences. Optionally, the software can analyze and filter previously generated baits. Besides, it did not have additional dependencies and does not require local compilation.
Detects barcodes and their abundances from raw next-generation sequencing data. Bartender employs a divide-and-conquer strategy that intelligently sorts barcode reads into distinct bins before performing comparisons, in order to improve speed and reduce unnecessary pairwise comparisons. To improve accuracy and reduce over-clustering artifacts, Bartender employs a modified two-sample proportion test that uses information on both the cluster sequence distances and cluster sizes to make merging decisions. Additionally, Bartender includes a “multiple time point” mode, which matches barcode clusters between different clustering runs for seamless handling of time course data.
Exploits genetic markers to perform taxonomic assignment. TAG ME is an R package, based on a multilevel supervised learning approach, able to perform a classification until species level. Users can build customized predictive models by using their own databases. The use of data from Illumina sequencing is recommended. It aims to assist users in understanding bacterial community structure and composition.
Provides tools and reports for the analysis of amplicon sequencing panels, such as AmpliSeq. AmpliQueso is a machine learning classifier evaluation of the answer to the question of difference between the patients and healthy donors, based upon the AmpliSeq panel data. The outcome confirms the potential utility of similar RNA amplicon kits in the research and clinical practice to encode gene expression signatures of diseases and their phenotypes.
Permits users to automate processing and haplotype inference for double-barcoded polymerase chain reaction (PCR) amplicons. Fluidigm2PURC uses methods that work on diploids, polyploids and individuals with unknown ploidy, or any mixture of the three. It is designed for investigation in taxa with incomplete knowledge about ploidy levels. This tool is based on a multinomial likelihood method to work.
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