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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.
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 language | English |
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Article number | 1287 |
Number of pages | 16 |
Journal | F1000Research |
Volume | 6 |
DOIs | |
Publication status | Published - 31 Jul 2017 |
Keywords / Materials (for Non-textual outputs)
- bioinformatics
- visualisation
- genome assembly
- quality control
- contaminant screening
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Dive into the research topics of 'BlobTools: Interrogation of genome assemblies'. Together they form a unique fingerprint.Projects
- 1 Finished
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Blobtoolkit: Identification and analysis of non-target and organisms in all Eukaryotic genome projects
Blaxter, M.
1/07/17 → 30/06/20
Project: Research
Datasets
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DRL/BlobTools_manuscript
Laetsch, D. (Creator), GitHub, 24 Jul 2017
DOI: 10.5281/zenodo.833879, https://github.com/DRL/blobtools_manuscript
Dataset