Detection of bacterial contaminants and hybrid sequences in the genome of the kelp Saccharina japonica using Taxoblast
Modern genome sequencing strategies are highly sensitive to contamination making the detection of foreign DNA sequences an important part of analysis pipelines. Here we use Taxoblast, a simple pipeline with a graphical user interface, for the post-assembly detection of contaminating sequences in the...
| Main Authors: | , |
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| Format: | Article |
| Language: | English |
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PeerJ Inc.
2017-11-01
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| Series: | PeerJ |
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| Online Access: | https://peerj.com/articles/4073.pdf |
| _version_ | 1797418587179188224 |
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| author | Simon M. Dittami Erwan Corre |
| author_facet | Simon M. Dittami Erwan Corre |
| author_sort | Simon M. Dittami |
| collection | DOAJ |
| description | Modern genome sequencing strategies are highly sensitive to contamination making the detection of foreign DNA sequences an important part of analysis pipelines. Here we use Taxoblast, a simple pipeline with a graphical user interface, for the post-assembly detection of contaminating sequences in the published genome of the kelp Saccharina japonica. Analyses were based on multiple blastn searches with short sequence fragments. They revealed a number of probable bacterial contaminations as well as hybrid scaffolds that contain both bacterial and algal sequences. This or similar types of analysis, in combination with manual curation, may thus constitute a useful complement to standard bioinformatics analyses prior to submission of genomic data to public repositories. Our analysis pipeline is open-source and freely available at http://sdittami.altervista.org/taxoblast and via SourceForge (https://sourceforge.net/projects/taxoblast). |
| first_indexed | 2024-03-09T06:35:02Z |
| format | Article |
| id | doaj.art-48654ab11dcb4895aa3e81057cef15a8 |
| institution | Directory Open Access Journal |
| issn | 2167-8359 |
| language | English |
| last_indexed | 2024-03-09T06:35:02Z |
| publishDate | 2017-11-01 |
| publisher | PeerJ Inc. |
| record_format | Article |
| series | PeerJ |
| spelling | doaj.art-48654ab11dcb4895aa3e81057cef15a82023-12-03T10:59:09ZengPeerJ Inc.PeerJ2167-83592017-11-015e407310.7717/peerj.4073Detection of bacterial contaminants and hybrid sequences in the genome of the kelp Saccharina japonica using TaxoblastSimon M. Dittami0Erwan Corre1UMR8227—Sorbonne Universités CNRS UPMC, Station Biologique de Roscoff, Roscoff, Brittany, FranceFR2424—Sorbonne Universités CNRS UPMC, Station Biologique de Roscoff, Roscoff, Brittany, FranceModern genome sequencing strategies are highly sensitive to contamination making the detection of foreign DNA sequences an important part of analysis pipelines. Here we use Taxoblast, a simple pipeline with a graphical user interface, for the post-assembly detection of contaminating sequences in the published genome of the kelp Saccharina japonica. Analyses were based on multiple blastn searches with short sequence fragments. They revealed a number of probable bacterial contaminations as well as hybrid scaffolds that contain both bacterial and algal sequences. This or similar types of analysis, in combination with manual curation, may thus constitute a useful complement to standard bioinformatics analyses prior to submission of genomic data to public repositories. Our analysis pipeline is open-source and freely available at http://sdittami.altervista.org/taxoblast and via SourceForge (https://sourceforge.net/projects/taxoblast).https://peerj.com/articles/4073.pdfBasic local alignment search tool (BLAST)Horizontal gene transferContaminating sequencesGenome assemblyBrown algae |
| spellingShingle | Simon M. Dittami Erwan Corre Detection of bacterial contaminants and hybrid sequences in the genome of the kelp Saccharina japonica using Taxoblast PeerJ Basic local alignment search tool (BLAST) Horizontal gene transfer Contaminating sequences Genome assembly Brown algae |
| title | Detection of bacterial contaminants and hybrid sequences in the genome of the kelp Saccharina japonica using Taxoblast |
| title_full | Detection of bacterial contaminants and hybrid sequences in the genome of the kelp Saccharina japonica using Taxoblast |
| title_fullStr | Detection of bacterial contaminants and hybrid sequences in the genome of the kelp Saccharina japonica using Taxoblast |
| title_full_unstemmed | Detection of bacterial contaminants and hybrid sequences in the genome of the kelp Saccharina japonica using Taxoblast |
| title_short | Detection of bacterial contaminants and hybrid sequences in the genome of the kelp Saccharina japonica using Taxoblast |
| title_sort | detection of bacterial contaminants and hybrid sequences in the genome of the kelp saccharina japonica using taxoblast |
| topic | Basic local alignment search tool (BLAST) Horizontal gene transfer Contaminating sequences Genome assembly Brown algae |
| url | https://peerj.com/articles/4073.pdf |
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