BlobTools: Interrogation of genome assemblies

Dominik R. Laetsch, Mark L. Blaxter

Research output: Contribution to journalArticlepeer-review

Abstract / Description of output

The goal of many genome sequencing projects is to provide a complete representation of a target genome (or genomes) as underpinning data for further analyses. However, it can be problematic to identify which sequences in an assembly truly derive from the target genome(s) and which are derived from associated microbiome or contaminant organisms. 

We present BlobTools, a modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets. Using guanine+cytosine content of sequences, read coverage in sequencing libraries and taxonomy of sequence similarity matches, BlobTools can assist in primary partitioning of data, leading to improved assemblies, and screening of final assemblies for potential contaminants. 

Through simulated paired-end read dataset,s containing a mixture of metazoan and bacterial taxa, we illustrate the main BlobTools workflow and suggest useful parameters for taxonomic partitioning of low-complexity metagenome assemblies.

Original languageEnglish
Article number1287
Number of pages16
Publication statusPublished - 31 Jul 2017

Keywords / Materials (for Non-textual outputs)

  • bioinformatics
  • visualisation
  • genome assembly
  • quality control
  • contaminant screening


Dive into the research topics of 'BlobTools: Interrogation of genome assemblies'. Together they form a unique fingerprint.

Cite this