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Quality assessment software tools | Shotgun metagenomic sequencing data analysis

Next-generation sequencing (NGS) technology has revolutionized and significantly impacted metagenomic research. However, the NGS data usually contains sequencing artifacts such as low-quality reads and contaminating reads, which will significantly…
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PRINSEQ
Desktop
Web

PRINSEQ PReprocessing and INformation of SEQuences

For easy and rapid quality control and data preprocessing of genomic and…

For easy and rapid quality control and data preprocessing of genomic and metagenomic datasets.

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Nonpareil
Desktop

Nonpareil

Estimate average coverage and create Nonpareil curves for metagenomic datasets.

Estimate average coverage and create Nonpareil curves for metagenomic datasets.

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TaxMan
Web

TaxMan

A xeb app which trims reference sequences based on user-selected primer pairs…

A xeb app which trims reference sequences based on user-selected primer pairs and returns an assessment of the primer specificity by taxa. TaxMan also provides graphical analysis of the taxa that are…

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NGS-eval
Web

NGS-eval

A user-friendly way to inspect NGS datasets obtained from the sequencing of…

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…

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mistagging
Desktop

mistagging

A software tool for removing biases and experimental planning for…

A software tool for removing biases and experimental planning for high-throughput sequencing (HTS) platforms. Being parameter-free and data-driven, this approach can provide more accurate and…

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fitGCP
Desktop

fitGCP

A framework for fitting mixtures of probability distributions to genome…

A framework for fitting mixtures of probability distributions to genome coverage profiles.

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EP_metagenomic
Desktop

EP_metagenomic

Calculates position and nucleotide-specific error profiles for metagenomic…

Calculates position and nucleotide-specific error profiles for metagenomic datasets. Current methods are not designed to target systematic errors in Illumina sequencing. In order to achieve any…

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MT-Toolbox
Desktop

MT-Toolbox Molecule Tag Toolbox

Provides an accessible, user-friendly environment for analysis of molecule…

Provides an accessible, user-friendly environment for analysis of molecule tagged reads thereby reducing technical errors and polymerase chain reaction bias. These improvements reduce noise and allow…

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StreamingTrim
Desktop

StreamingTrim

A DNA reads trimming software, written in Java, with which researchers are able…

A DNA reads trimming software, written in Java, with which researchers are able to analyse the quality of DNA sequences in fastq files and to search for low-quality zones in a very conservative way.

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KneadData
Desktop

KneadData

Aims to perform principled in silico separation of bacterial reads from these…

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,…

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MESER
Web

MESER Miseq Erroneous SEquence Removal

A web interface that allows users to conduct fastq-merging and mothur batch…

A web interface that allows users to conduct fastq-merging and mothur batch creation.

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PathoQC
Desktop

PathoQC

Pre-processes next-generation sequencing (NGS) data. PathoQC is based on…

Pre-processes next-generation sequencing (NGS) data. PathoQC is based on several of the most used quality control software approaches and combines their benefits to offer a variety of quality control…

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Meta-QC-Chain
Desktop

Meta-QC-Chain

Provides a comprehensive, useful and high-performance QC tool for metagenomic…

Provides a comprehensive, useful and high-performance QC tool for metagenomic data.

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