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...
| Main Authors: | , , |
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| Format: | Online |
| Language: | English |
| Published: |
Oxford University Press
2013
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| Online Access: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3546798/ |
| Summary: | 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. |
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