High-throughput microbial population genomics using the Cortex variation assembler.
SUMMARY: We have developed a software package, Cortex, designed for the analysis of genetic variation by de novo assembly of multiple samples. This allows direct comparison of samples without using a reference genome as intermediate and incorporates discovery and genotyping of single-nucleotide poly...
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| Format: | Journal article |
| Language: | English |
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Oxford University Press
2013
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| _version_ | 1797094189947682816 |
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| author | Iqbal, Z Turner, I Mcvean, G |
| author_facet | Iqbal, Z Turner, I Mcvean, G |
| author_sort | Iqbal, Z |
| collection | OXFORD |
| description | SUMMARY: We have developed a software package, Cortex, designed for the analysis of genetic variation by de novo assembly of multiple samples. This allows direct comparison of samples without using a reference genome as intermediate and incorporates discovery and genotyping of single-nucleotide polymorphisms, indels and larger events in a single framework. We introduce pipelines which simplify the analysis of microbial samples and increase discovery power; these also enable the construction of a graph of known sequence and variation in a species, against which new samples can be compared rapidly. We demonstrate the ease-of-use and power by reproducing the results of studies using both long and short reads. AVAILABILITY: http://cortexassembler.sourceforge.net (GPLv3 license). CONTACT: zam@well.ox.ac.uk, mcvean@well.ox.ac.uk SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. |
| first_indexed | 2024-03-07T04:10:37Z |
| format | Journal article |
| id | oxford-uuid:c7b57beb-3bb3-498b-af45-caca31f1b361 |
| institution | University of Oxford |
| language | English |
| last_indexed | 2024-03-07T04:10:37Z |
| publishDate | 2013 |
| publisher | Oxford University Press |
| record_format | dspace |
| spelling | oxford-uuid:c7b57beb-3bb3-498b-af45-caca31f1b3612022-03-27T06:47:02ZHigh-throughput microbial population genomics using the Cortex variation assembler.Journal articlehttp://purl.org/coar/resource_type/c_dcae04bcuuid:c7b57beb-3bb3-498b-af45-caca31f1b361Bioinformatics (biochemistry)EnglishSymplectic Elements at OxfordOxford University Press2013Iqbal, ZTurner, IMcvean, GSUMMARY: We have developed a software package, Cortex, designed for the analysis of genetic variation by de novo assembly of multiple samples. This allows direct comparison of samples without using a reference genome as intermediate and incorporates discovery and genotyping of single-nucleotide polymorphisms, indels and larger events in a single framework. We introduce pipelines which simplify the analysis of microbial samples and increase discovery power; these also enable the construction of a graph of known sequence and variation in a species, against which new samples can be compared rapidly. We demonstrate the ease-of-use and power by reproducing the results of studies using both long and short reads. AVAILABILITY: http://cortexassembler.sourceforge.net (GPLv3 license). CONTACT: zam@well.ox.ac.uk, mcvean@well.ox.ac.uk SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online. |
| spellingShingle | Bioinformatics (biochemistry) Iqbal, Z Turner, I Mcvean, G High-throughput microbial population genomics using the Cortex variation assembler. |
| title | High-throughput microbial population genomics using the Cortex variation assembler. |
| title_full | High-throughput microbial population genomics using the Cortex variation assembler. |
| title_fullStr | High-throughput microbial population genomics using the Cortex variation assembler. |
| title_full_unstemmed | High-throughput microbial population genomics using the Cortex variation assembler. |
| title_short | High-throughput microbial population genomics using the Cortex variation assembler. |
| title_sort | high throughput microbial population genomics using the cortex variation assembler |
| topic | Bioinformatics (biochemistry) |
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