BlobTools: Interrogation of genome assemblies

By Dominik R. Laetsch, Mark L. Blaxter. F1000Research, 2017

837 citations recorded by the source corpus.

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.

Subfields: Ecology, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/20c417033a2d394e24cbc7a0c27029c1a31a69fd

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Citations in the corpus

BlobToolKit – Interactive Quality Assessment of Genome Assemblies (2019, methodology): “BlobTools2 is a re-implementation of BlobTools (Laetsch and Blaxter 2017), written in python3 and based around a BlobDir directory of JSON format ﬁ les.”