diff --git a/paper/paper.bib b/paper/paper.bib index 2970e6b..3df5c61 100644 --- a/paper/paper.bib +++ b/paper/paper.bib @@ -21,3 +21,16 @@ @article{10.1093/nar/gks596 doi = {10.1093/nar/gks596}, url = {https://doi.org/10.1093/nar/gks596} } + +@article{10.1093/bib/bbs038, + author = {{Khun}, Robert M. and {Haussler}, David and {Kent}, James}, + title = "{The UCSC genome browser and associated tools}", + journal = {Briefings in Bioinformatics}, + volume = {14}, + number = {2}, + year = {2012}, + issn = {1467-5463}, + doi = {10.1093/bib/bbs038}, + url = {https://doi.org/10.1093/bib/bbs038} +} +} diff --git a/paper/paper.md b/paper/paper.md index c67ac2c..65f3692 100644 --- a/paper/paper.md +++ b/paper/paper.md @@ -62,7 +62,9 @@ from another set of genomes via PCR amplification. `primerForge` relies on the `khmer` package to extract k-mers from genomic sequences and the `primer3-py` package to evaluate specific characteristics of primer pairs including melting temperature, hairpin potential, and dimer formation -[@10.12688/f1000research.6924.1; @10.1093/nar/gks596]. +[@10.12688/f1000research.6924.1; @10.1093/nar/gks596]. It also uses _in silico_ +PCR via the `isPcr` program to validate and filter the primer pairs +[@10.1093/bib/bbs038]. There are many use cases for what `primerForge` offers. One use case would be surveillance of an outbreak clone of a particular pathogen. A laboratory could