BlobToolKit – Interactive Quality Assessment of Genome Assemblies

Abstract

Reconstruction of target genomes from sequence data produced by instruments that are agnostic as to the species-of-origin may be confounded by contaminant DNA. Whether introduced during sample processing or through co-extraction alongside the target DNA, if insufficient care is taken during the assembly process, the final assembled genome may be a mixture of data from several species. Such assemblies can confound sequence-based biological inference and, when deposited in public databases, may be included in downstream analyses by users unaware of underlying problems. We present BlobToolKit, a software suite to aid researchers in identifying and isolating non-target data in draft and publicly available genome assemblies. BlobToolKit can be used to process assembly, read and analysis files for fully reproducible interactive exploration in the browser-based Viewer. BlobToolKit can be used during assembly to filter non-target DNA, helping researchers produce assemblies with high biological credibility. We have been running an automated BlobToolKit pipeline on eukaryotic assemblies publicly available in the International Nucleotide Sequence Data Collaboration and are making the results available through a public instance of the Viewer at https://blobtoolkit.genomehubs.org/view. We aim to complete analysis of all publicly available genomes and then maintain currency with the flow of new genomes. We have worked to embed these views into the presentation of genome assemblies at the European Nucleotide Archive, providing an indication of assembly quality alongside the public record with links out to allow full exploration in the Viewer.

A telomere to telomere assembly ofOscheius tipulaeand the evolution of rhabditid nematode chromosomes

“…B. BlobToolKit (Challis et al, 2020) plot (GC proportion [x axis] vestus read coverage [y axis]) of the flye assembly of all the sequenced reads. Taxonomic annotation was achieved using blastx and Diamond tblastn source classification.…”

Significantly improving the quality of genome assemblies through curation

“…This includes identifying remaining vector and adapter contamination based on known sequence. Contaminating sequence can be detected with dedicated toolkits, such as BlobToolKit [18] or Anvi'o [19] or through individual sequence similarity searches using BLAST or Diamond against suitable databases (Table 1). Our in-house pipelines use automated detection of synthetic, laboratory and natural contaminants, but include manual controls to preserve sequences that may be the product of horizontal gene transfer (described below).…”

Biodiversity genomics of small metazoans: high qualityde novogenomes from single specimens of field-collected and ethanol-preserved springtails

“…Finally, we used ncbi-blastn to query the contigs against the NCBI nr nucleotide database (-max_target_seqs 10 -max_hsps 1 -evalue 1e-25). We used the BlobToolKit pipeline (Challis, Richards, Rajan, Cochrane & Blaxter, 2020) to merge and plot the DIAMOND and BLAST taxonomic assignment with the assembly statistics (GC content and base coverage). Contigs explicitly assigned to anything else than metazoan were excluded from downstream analysis.…”