BlobToolKit

BlobToolKit identifies and separates contaminant and non-target sequences from draft and publicly available genome assemblies to improve assembly quality and downstream biological inference.

Key Features:

• Contaminant identification: Distinguishes target genomes from contaminant DNA in assemblies to prevent mixed-species assemblies and erroneous biological inference.
• Visualization and exploration of genome-scale datasets: Provides visualization and exploration capabilities for genome-scale datasets to assist in identifying and filtering target and non-target data.
• Reproducible processing: Processes assembly, read, and analysis files in a manner that supports reproducible research and consistent results.
• Automated pipeline for INSDC assemblies: Implements an automated pipeline to process eukaryotic assemblies available through the International Nucleotide Sequence Data Collaboration.
• Integration with public databases (ENA): Embeds BlobToolKit views into the presentation of genome assemblies at the European Nucleotide Archive (ENA) to provide assembly-quality context alongside the public record.

Scientific Applications:

• Genome assembly quality assessment: Detects and separates non-target DNA to produce assemblies that more accurately represent the biological entity under study.
• Metagenomic and mixed-sample analysis: Filters non-target sequences in metagenomic datasets and samples with high microbial diversity to reduce false-positive assemblies.
• Public data curation and quality annotation: Supplies quality assessments and visualizations for publicly available genomes and supports ongoing evaluation of assemblies in public repositories such as ENA.

Methodology:

Processes assembly, read, and analysis files to identify and isolate contaminant or non-target sequences and implements an automated pipeline for processing eukaryotic assemblies from the International Nucleotide Sequence Data Collaboration.