ESSENTIALS: software for rapid analysis of high throughput transposon insertion sequencing data.
High-throughput analysis of genome-wide random transposon mutant libraries is a powerful tool for (conditional) essential gene discovery. Recently, several next-generation sequencing approaches, e.g. Tn-seq/INseq, HITS and TraDIS, have been developed that accurately map the site of transposon insert...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2012-01-01
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| Series: | PLoS ONE |
| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22900082/pdf/?tool=EBI |
| _version_ | 1818742660696899584 |
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| author | Aldert Zomer Peter Burghout Hester J Bootsma Peter W M Hermans Sacha A F T van Hijum |
| author_facet | Aldert Zomer Peter Burghout Hester J Bootsma Peter W M Hermans Sacha A F T van Hijum |
| author_sort | Aldert Zomer |
| collection | DOAJ |
| description | High-throughput analysis of genome-wide random transposon mutant libraries is a powerful tool for (conditional) essential gene discovery. Recently, several next-generation sequencing approaches, e.g. Tn-seq/INseq, HITS and TraDIS, have been developed that accurately map the site of transposon insertions by mutant-specific amplification and sequence readout of DNA flanking the transposon insertions site, assigning a measure of essentiality based on the number of reads per insertion site flanking sequence or per gene. However, analysis of these large and complex datasets is hampered by the lack of an easy to use and automated tool for transposon insertion sequencing data. To fill this gap, we developed ESSENTIALS, an open source, web-based software tool for researchers in the genomics field utilizing transposon insertion sequencing analysis. It accurately predicts (conditionally) essential genes and offers the flexibility of using different sample normalization methods, genomic location bias correction, data preprocessing steps, appropriate statistical tests and various visualizations to examine the results, while requiring only a minimum of input and hands-on work from the researcher. We successfully applied ESSENTIALS to in-house and published Tn-seq, TraDIS and HITS datasets and we show that the various pre- and post-processing steps on the sequence reads and count data with ESSENTIALS considerably improve the sensitivity and specificity of predicted gene essentiality. |
| first_indexed | 2024-12-18T02:16:03Z |
| format | Article |
| id | doaj.art-805561fa1c3846d6a54e7c175dc04764 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-18T02:16:03Z |
| publishDate | 2012-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-805561fa1c3846d6a54e7c175dc047642022-12-21T21:24:23ZengPublic Library of Science (PLoS)PLoS ONE1932-62032012-01-0178e4301210.1371/journal.pone.0043012ESSENTIALS: software for rapid analysis of high throughput transposon insertion sequencing data.Aldert ZomerPeter BurghoutHester J BootsmaPeter W M HermansSacha A F T van HijumHigh-throughput analysis of genome-wide random transposon mutant libraries is a powerful tool for (conditional) essential gene discovery. Recently, several next-generation sequencing approaches, e.g. Tn-seq/INseq, HITS and TraDIS, have been developed that accurately map the site of transposon insertions by mutant-specific amplification and sequence readout of DNA flanking the transposon insertions site, assigning a measure of essentiality based on the number of reads per insertion site flanking sequence or per gene. However, analysis of these large and complex datasets is hampered by the lack of an easy to use and automated tool for transposon insertion sequencing data. To fill this gap, we developed ESSENTIALS, an open source, web-based software tool for researchers in the genomics field utilizing transposon insertion sequencing analysis. It accurately predicts (conditionally) essential genes and offers the flexibility of using different sample normalization methods, genomic location bias correction, data preprocessing steps, appropriate statistical tests and various visualizations to examine the results, while requiring only a minimum of input and hands-on work from the researcher. We successfully applied ESSENTIALS to in-house and published Tn-seq, TraDIS and HITS datasets and we show that the various pre- and post-processing steps on the sequence reads and count data with ESSENTIALS considerably improve the sensitivity and specificity of predicted gene essentiality.https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22900082/pdf/?tool=EBI |
| spellingShingle | Aldert Zomer Peter Burghout Hester J Bootsma Peter W M Hermans Sacha A F T van Hijum ESSENTIALS: software for rapid analysis of high throughput transposon insertion sequencing data. PLoS ONE |
| title | ESSENTIALS: software for rapid analysis of high throughput transposon insertion sequencing data. |
| title_full | ESSENTIALS: software for rapid analysis of high throughput transposon insertion sequencing data. |
| title_fullStr | ESSENTIALS: software for rapid analysis of high throughput transposon insertion sequencing data. |
| title_full_unstemmed | ESSENTIALS: software for rapid analysis of high throughput transposon insertion sequencing data. |
| title_short | ESSENTIALS: software for rapid analysis of high throughput transposon insertion sequencing data. |
| title_sort | essentials software for rapid analysis of high throughput transposon insertion sequencing data |
| url | https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22900082/pdf/?tool=EBI |
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