Sharkmer: repurposing PCR primers for targeted genome assembly using in silico PCR.
basic_science · Level V
Where this comes from
- Record sourced from PubMed, PMID 41955310.
- Also identified by DOI 10.1093/bioinformatics/btag163 and PMC identifier 13090824.
- Licence recorded as CC BY.
- The licence permits redistribution, so the abstract is shown in full and the full text is available from the publisher.
Abstract
We introduce an in silico PCR (sPCR) method for the assembly of specific genomic regions spanned by PCR primers using raw sequence reads. This allows a user to quickly isolate the exact regions that are abundant in public archives of gene sequences, leveraging the decades of work that have gone into optimizing primer sequences for benchtop PCR. We implement sPCR in sharkmer as a targeted de Bruijn graph assembler seeded with the forward primer sequence and terminated with the reverse primer sequence. This is useful for a variety of routine tasks, including validating the species identity of a dataset, identifying contaminants, and quickly building phylogenies from raw sequence data. sharkmer is written in Rust. Code, instructions for installation and use, tests, and other resources are available in the GitHub repository at https://github.com/caseywdunn/sharkmer and at Zenodo with DOI 10.5281/zenodo.19020708. It can also be installed via bioconda.
Medical subject headings
- Software
- DNA Primers
- Polymerase Chain Reaction
- Genomics
- Sequence Analysis, DNA
- Genome