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Sequence contamination detection software tools | Shotgun metagenomic sequencing data analysis

High-throughput sequencing technologies have strongly impacted microbiology, providing a rapid and cost-effective way of generating draft genomes and exploring microbial diversity. However, sequences obtained from impure nucleic acid preparations…
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SeqClean
Desktop

SeqClean

Removes any sequence highly similar to a given list of vectors, adaptors,…

Removes any sequence highly similar to a given list of vectors, adaptors, primers, or linker sequences. SeqClean was created to clean databases when specific vector and splice site data are not…

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Vecuum
Desktop

Vecuum

A Java based variant caller designed for detecting contamination-induced point…

A Java based variant caller designed for detecting contamination-induced point mutations from hybrid-capture-based genome sequencing data (WGS, WES, targeted capture, etc). Vecuum is specialized for…

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AFS
Desktop

AFS All-Food-Seq

Quantifies species composition in food. AFS uses metagenomic shotgun sequencing…

Quantifies species composition in food. AFS uses metagenomic shotgun sequencing and sequence read counting to infer species proportions. It screens for species composition and relative quantities via…

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DeconSeq
Desktop

DeconSeq

It can be used to automatically detect and efficiently remove sequence…

It can be used to automatically detect and efficiently remove sequence contaminations from genomic and metagenomic datasets.

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ContEst
Desktop

ContEst

A tool (and method) for estimating the amount of cross-sample contamination in…

A tool (and method) for estimating the amount of cross-sample contamination in next generation sequencing data.

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PhylOligo
Desktop

PhylOligo

Detects contaminant DNA by exploring oligonucleotide composition similarity…

Detects contaminant DNA by exploring oligonucleotide composition similarity between assembly contigs or scaffolds. PhylOligo generates an all-by-all contig distance matrix and regroups contigs by…

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MCSC
Desktop

MCSC Model-based Categorical Sequence Clustering

Provides an efficient way to decontaminate assemblies from non-model organisms…

Provides an efficient way to decontaminate assemblies from non-model organisms by using the information contained in the sequences themselves. MCSC is a decontamination method based on a hierarchical…

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HYSYS
Desktop

HYSYS Have You Swapped Your Samples

A statistical method to estimate the relatedness of samples and test for sample…

A statistical method to estimate the relatedness of samples and test for sample swaps and contamination. The test uses the concordance of homozygous single-nucleotide polymorphisms between samples.…

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Conpair
Desktop

Conpair Concordance/Contamination of paired samples

A tool for detection of sample swaps and cross-individual contamination in…

A tool for detection of sample swaps and cross-individual contamination in whole-genome and whole-exome tumor–normal sequencing experiments. Conpair is a fast and robust method dedicated for human…

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VecScreen_plus_…
Desktop

VecScreen_plus_taxonomy

Makes the classification of VecScreen matches into true and false matches…

Makes the classification of VecScreen matches into true and false matches automatically and deterministically. VecScreen_plus_taxonomy compares submitted nucleotide sequence(s) as a query to a…

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ACDC
Web
Desktop

ACDC Automated Contamination Detection and Confidence estimation

Detects both known and de novo contaminants. ACDC was specifically developed to…

Detects both known and de novo contaminants. ACDC was specifically developed to aid the quality control process of genomic sequence data. First, 16S rRNA gene prediction and the inclusion of…

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MIDAS
Desktop

MIDAS Metagenomic Intra-species Diversity Analysis System

Allows users to measure bacterial strain-level gene content, single nucleotide…

Allows users to measure bacterial strain-level gene content, single nucleotide polymorphism (SNPs) and species abundance from shotgun metagenomes. MIDAS is able to determine genetic variants into…

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PhagePhisher
Desktop

PhagePhisher

Extracts relevant information from complex and mixed datasets. PhagePhisher…

Extracts relevant information from complex and mixed datasets. PhagePhisher improves the examination of bacteriophages, viruses, and virally related sequences, in a range of environments. It can be…

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VecScreen
Web

VecScreen

Finds segments of a nucleic acid sequence that could be of vector origin.…

Finds segments of a nucleic acid sequence that could be of vector origin. VecScreen helps researchers to identify and remove any segments of vector origin before they analyse or submit sequences. It…

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Nullarbor
Desktop

Nullarbor

A pipeline to generate complete public health microbiology reports from…

A pipeline to generate complete public health microbiology reports from sequenced isolates. Nullarbor currently only supports Illumina paired-end sequencing data; single end reads, from either…

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Cookiecutter
Desktop

Cookiecutter

A computational tool for rapid read extraction or removing according to a…

A computational tool for rapid read extraction or removing according to a provided list of k-mers generated from a FASTA file. Cookiecutter is based on the implementation of the Aho-Corasik algorithm…

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vectorstrip
Desktop

vectorstrip

Removes vectors from the ends of one or more nucleotide sequences. vectorstrip…

Removes vectors from the ends of one or more nucleotide sequences. vectorstrip writes nucleotide sequences out again but with any of a specified set of vector sequences removed from the 5' and…

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UniVec
Dataset

UniVec

Identifies segments within nucleic acid sequences which may be of vector…

Identifies segments within nucleic acid sequences which may be of vector origin. UniVec is an efficient database because a large number of redundant subsequences have been eliminated to create a…

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Blobology
Desktop

Blobology

Extracts, from mixed DNA sequence data, subsets that correspond to single…

Extracts, from mixed DNA sequence data, subsets that correspond to single species’ genomes and thus improving genome assembly. Blobology aims to create blobplots or Taxon-Annotated GC-Coverage…

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Eu-Detect
Web

Eu-Detect

An alignment-free algorithm that can rapidly identify eukaryotic sequences…

An alignment-free algorithm that can rapidly identify eukaryotic sequences contaminating metagenomic data sets. Validation results indicate that, even on a desktop with modest hardware…

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QC-Chain
Desktop

QC-Chain

A fast, accurate and holistic NGS data quality-control method. The tool…

A fast, accurate and holistic NGS data quality-control method. The tool synergeticly comprised of user-friendly tools for (1) quality assessment and trimming of raw reads using Parallel-QC, a fast…

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CS-SCORE
Desktop

CS-SCORE

Identifies host sequences contaminating metagenomic datasets. Validation…

Identifies host sequences contaminating metagenomic datasets. Validation results indicate that CS-SCORE is 2-6 times faster than the current state-of-the-art methods. Furthermore, the memory…

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