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NGS-eval

A user-friendly way to inspect NGS datasets obtained from the sequencing of genetic markers in microbial communities. The error calculation functionality enables the evaluation of the overall sequencing quality and can further be used to assess the outcome of NGS data processing pipelines. The interactive plots in NGS-eval quickly illustrate the read coordinates where the errors occur. High frequency of errors at specific positions can be useful for detecting novel (common) sequence variants and identifying the differences between the strains that are present in the sample and that are used as reference sequences.

A-GAME / A GAlaxy suite for functional MEtagenomics

New
Incorporates tools and workflows for the analysis of environmental DNA (eDNA) sequence data. A-GAME is a general bioinformatics workflow management system implemented within Galaxy. The software contains pre-designed workflows that utilize standard tools for data pre-processing, sequence assembly and annotation; as well as custom utilities dedicated to the analysis of functional metagenomics data. It allows the incorporation of most widely used bioinformatics tools. A-GAME can be used to build and customize bioinformatics workflows.

KneadData

Aims to perform principled in silico separation of bacterial reads from these "contaminant" reads. KneadData is a tool designed to perform quality control on metagenomic sequencing data, especially data from microbiome experiments. In these experiments, samples are typically taken from a host in hopes of learning something about the microbial community on the host. Additionally, KneadData can be used for other filtering tasks. For example, if one is trying to clean data derived from a human sequencing experiment, KneadData can be used to separate the human and the non-human reads.