Citing the Palfinder Galaxy Service

Please cite the following reference if you use this service or the bioinformatics pipeline described for microsatellite development:

• Griffiths SM, Fox G, Briggs PJ, Donaldson IJ, Hood S, Richardson P, Leaver GW, Truelove NK & Preziosi RF (2016) A Galaxy-based bioinformatics pipeline for optimised, streamlined microsatellite development from Illumina next-generation sequencing data. Conservation Genetics Resources
  doi:10.1007/s12686-016-0570-7

In addition the the individual programs in the pipeline should be cited:

Pal_finder:
Castoe T, Poole A, de Koning A (2012) Rapid microsatellite identification from Illumina paired-end genomic sequencing in two birds and a snake. PLoS One 7:e3095. doi: 10.1371/journal.pone.0030953.

Primer3:
Koressaar T, Remm M (2007) Enhancements and modifications of primer design program Primer3. Bioinformatics 23:1289–91. doi: 10.1093/bioinformatics/btm091
Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, Rozen SG (2012) Primer3 - new capabilities and interfaces. Nucleic Acids Res 40:e115. doi: 10.1093/nar/gks596

PANDASeq:
Masella AP, Bartram AK, Truszkowski JM, Brown DG, Neufeld JD (2012) PANDAseq: paired-end assembler for Illumina sequences. BMC Bioinformatics 13:31. doi: 10.1186/1471-2105-13-31

Trimmomatic:
Bolger AM, Lohse M, Usadel B (2014) Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30:2114-20. doi: 10.1093/bioinformatics/btu170

FastQC:
Andrews S. (2010). FastQC a Quality Control Tool for High Throughput Sequence Data [Online]. Available online at: http://www.bioinformatics.babraham.ac.uk/projects/fastqc/

Instructions for citing Galaxy can be found here on the Galaxy website.