Update README.md

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CalCOFI · Jun 21, 2024 · 4c0aa90 · 4c0aa90
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diff --git a/README.md b/README.md
@@ -928,12 +928,12 @@ derep_and_clean_db(output_directory_path, summary_path, metabarcode_name)
 | Primer Name	| Gene  | Length of Target | get_seeds_local() length minimum | get_seeds_local() length maximum | blast_seeds() length minimum | blast_seeds() length maximum | blast_seeds() max_to_blast | Forward Sequence (5'-3') | Reverse Sequence (5'-3') | Reference | Zenodo Link |
 | ------------- | ------------- | ------------- | ------------- |------------- | ------------- |------------- | ------------- |------------- | ------------- |------------- |		------------- |		
 |[MiFish Universal](https://doi.org/10.5281/zenodo.7909637)	| 12S	| 163–185|	170	| 250 |	140	|250	|1000	|GTGTCGGTAAAACTCGTGCCAGC |	CATAGTGGGGTATCTAATCCCAGTTTG	|Miya, M., Sato, Y., Fukunaga, T., Sado, T., Poulsen, J. Y., Sato, K., ... & Kondoh, M. (2015). MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species. Royal Society open science, 2(7), 150088.|	https://doi.org/10.5281/zenodo.7909637		|
-|[MiFish Universal Expanded](|https://doi.org/10.5281/zenodo.7908864)	|12S|	163–185|	170|	250|	140|	250|	1000|	GTGTCGGTAAAACTCGTGCCAGC|	CATAGTGGGGTATCTAATCCCAGTTTG	|Miya, M., Sato, Y., Fukunaga, T., Sado, T., Poulsen, J. Y., Sato, K., ... & Kondoh, M. (2015). MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species. Royal Society open science, 2(7), 150088.	|https://doi.org/10.5281/zenodo.7908864		|
+|[MiFish Universal Expanded](https://doi.org/10.5281/zenodo.7908864)	|12S|	163–185|	170|	250|	140|	250|	1000|	GTGTCGGTAAAACTCGTGCCAGC|	CATAGTGGGGTATCTAATCCCAGTTTG	|Miya, M., Sato, Y., Fukunaga, T., Sado, T., Poulsen, J. Y., Sato, K., ... & Kondoh, M. (2015). MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species. Royal Society open science, 2(7), 150088.	|https://doi.org/10.5281/zenodo.7908864		|
 |[Kelly 16s](https://doi.org/10.5281/zenodo.7909659)|	16S|	114-160	|80|	195|	50|	168|	100	|AGTTACYYTAGGGATAACAGCG	|CCGGTCTGAACTCAGATCAYGT	|Kelly, R. P., O’Donnell, J. L., Lowell, N. C., Shelton, A. O., Samhouri, J. F., Hennessey, S. M., ... & Williams, G. D. (2016). Genetic signatures of ecological diversity along an urbanization gradient. PeerJ, 4, e2444.|	https://doi.org/10.5281/zenodo.7909659		|
 |[Ford 16S](https://doi.org/10.5281/zenodo.7909642)	|16S	|330	|279	|477|	231	|429	|1000|	GCAATCACTTGTCTTTTAAATGAAGACC, GTAATCACTTGTCTTTTAAATGAAGACC|	GGATTGCGCTGTTATCCCTA|	Ford MJ, Hempelmann J, Hanson MB, Ayres KL, Baird RW, et al. (2016) Estimation of a Killer Whale (Orcinus orca) Population’s Diet Using Sequencing Analysis of DNA from Feces. PLOS ONE 11(1): e0144956. https://doi.org/10.1371/journal.pone.0144956|	https://doi.org/10.5281/zenodo.7909642	|	
 |[MarVer3](https://doi.org/10.5281/zenodo.7909663)	|16S	|232-274|	160|	345	|124|	309|	100|	AGACGAGAAGACCCTRTG|	GGATTGCGCTGTTATCCC|	Valsecchi, E., Bylemans, J., Goodman, S. J., Lombardi, R., Carr, I., Castellano, L., ... & Galli, P. (2020). Novel universal primers for metabarcoding environmental DNA surveys of marine mammals and other marine vertebrates. Environmental DNA, 2(4), 460-476.|	https://doi.org/10.5281/zenodo.7909663	|	
 |[MiDeca](https://doi.org/10.5281/zenodo.7909669) |	16S|	154-184	|105	|230|	66|	191|	50|	GGACGATAAGACCCTATAAA	|ACGCTGTTATCCCTAAAGT|	Komai, Tomoyuki, et al. "Development of a new set of PCR primers for eDNA metabarcoding decapod crustaceans." Metabarcoding and Metagenomics 3 (2019): e33835.|	https://doi.org/10.5281/zenodo.7909669|		
-|[Ceph18S[]()](https://doi.org/10.5281/zenodo.7909639)	|18S	|150-190	|105	|235|	65|	195|	100|	CGCGGCGCTACATATTAGAC|	GCACTTAACCGACCGTCGAC|	D. S. W. de Jonge, V. Merten, T. Bayer, O. Puebla, T. B. H. Reusch, H.-J. T. Hoving, A novel metabarcoding primer pair for environmental DNA analysis of Cephalopoda (Mollusca) targeting the nuclear 18S rRNA region. R. Soc. Open Sci. 8, 201388 (2021)	|https://doi.org/10.5281/zenodo.7909639	|	
+|[Ceph18S](https://doi.org/10.5281/zenodo.7909639)	|18S	|150-190	|105	|235|	65|	195|	100|	CGCGGCGCTACATATTAGAC|	GCACTTAACCGACCGTCGAC|	D. S. W. de Jonge, V. Merten, T. Bayer, O. Puebla, T. B. H. Reusch, H.-J. T. Hoving, A novel metabarcoding primer pair for environmental DNA analysis of Cephalopoda (Mollusca) targeting the nuclear 18S rRNA region. R. Soc. Open Sci. 8, 201388 (2021)	|https://doi.org/10.5281/zenodo.7909639	|	
 |[Scott Baker Dlp1.5-H/Oordlp4](https://doi.org/10.5281/zenodo.7909691)|	D loop|	350-390	|245|	495|	205|	455|	100	|TCACCCAAAGCTGRARTTCTA|	GCGGGTTGCTGGTTTCACG	|Baker, C. S., Steel, D., Nieukirk, S., & Klinck, H. (2018). Environmental DNA (eDNA) from the wake of the whales: Droplet digital PCR for detection and species identification. Frontiers in Marine Science, 5, 133.|	https://doi.org/10.5281/zenodo.7909691|
 |[ITS2 Plants](https://doi.org/10.5281/zenodo.7909655)	|ITS2	|450 to 550 bp	|315	|600	|270	|560	|100	|ATGCGATACTTGGTGTGAAT	|GACGCTTCTCCAGACTACAAT|	Gu, W., Song, J., Cao, Y., Sun, Q., Yao, H., Wu, Q., ... & Duan, J. (2013). Application of the ITS2 region for barcoding medicinal plants of Selaginellaceae in Pteridophyta. PloS one, 8(6), e67818.|	https://doi.org/10.5281/zenodo.7909655 |
 |[trnl plants](https://doi.org/10.5281/zenodo.7909700)|	trnl|	~85bp	|60	|110|	23	|73|	250	|GGGCAATCCTGAGCCAA|	TTTGAGTCTCTGCACCTATC|	Coissac, E., Pompanon, F., Gielly, L., Miquel, C., Valentini, A., Vermat, T., ... & Willerslev, E. (2007). Power and limitations of the chloroplast trnL (UAA) intron for plant DNA barcoding. Nucleic Acids Research 3 (35),.(2007).|	https://doi.org/10.5281/zenodo.7909700	|