Metagenomics Contaminant Removal with Bowtie

Metagenomics Contaminant Removal with Bowtie


A common preprocessing step in metagenomics data analysis e.g. working with host-associated studies is to remove the host-related DNA from the sequencing data. This is often referred to as contamination removal. A common approach to isolate host-related reads is performing a read mapping against the host genome. Bowtie2 is the reference tool for this task.

Since OmicsBox 2.0 this feature is available in the Metagenomics Module.

Contaminant Removal with Bowtie 2 in OmicsBox

  • The Contaminant Removal tools accepts NGS reads in fasta, fastq single, and fastq paired-end format and separates the dataset into 2 parts, contaminant and contaminant-free reads. The output consists of files containing the separated reads.
  • OmicsBox allows contaminant screening for a few preconfigured organisms: Human, Mouse, PhiX, etc. Custom target databases of any organism can be uploaded in fasta format.
  • The output can directly be used for further analysis steps like taxonomic quantification with Kraken.
Note: The contaminant removal process as a taxonomic classification preprocessing step helps to reduce the number of unclassified and misclassified reads.
Note: The contaminant removal process can be repeated multiple times for further refinement (e.g. with different phylogenetically close target genomes).


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Contaminant Removal with Bowtie2 in OmicsBox
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