Update refs including seqwho to biorxiv

docs/references.md

@@ -4,28 +4,28 @@
   * Anaconda (Anaconda Software Distribution, [https://anaconda.com](https://anaconda.com))
 
 2. **DERIVA**:
-  * Bugacov, A., Czajkowski, K., Kesselman, C., Kumar,  A., Schuler, R. E. and Tangmunarunkit, H. 2017 Experiences with DERIVA: An Asset Management Platform for Accelerating eScience. IEEE 13th International Conference on e-Science (e-Science), Auckland, 2017, pp. 79-88, doi:[10.1109/eScience.2017.20](https://doi.org/10.1109/eScience.2017.20).
+  * Bugacov, A., Czajkowski, K., Kesselman, C., Kumar, A., Schuler, R. E., & Tangmunarunkit, H. (2017, October). Experiences with DERIVA: An asset management platform for accelerating eScience. In 2017 IEEE 13th International Conference on e-Science (e-Science) (pp. 79-88). IEEE. doi:[10.1109/eScience.2017.20](https://doi.org/10.1109/eScience.2017.20).
 
 3. **BDBag**:  
-  * D'Arcy, M., Chard, K., Foster, I., Kesselman, C., Madduri, R., Saint, N., & Wagner, R.. 2019. Big Data Bags: A Scalable Packaging Format for Science. Zenodo. doi:[10.5281/zenodo.3338725](http://doi.org/10.5281/zenodo.3338725).
+  * Madduri, R., Chard, K., D’Arcy, M., Jung, S. C., Rodriguez, A., Sulakhe, D., ... & Foster, I. (2019). Reproducible big data science: A case study in continuous FAIRness. PloS one, 14(4), e0213013. doi:[10.1371/journal.pone.0213013](https://doi.org/10.1371/journal.pone.0213013).
 
 4. **trimgalore**:
   * trimgalore [https://github.com/FelixKrueger/TrimGalore](https://github.com/FelixKrueger/TrimGalore)
 
 5. **hisat2**:
-  * Kim ,D.,Paggi, J.M., Park, C., Bennett, C., Salzberg, S.L. 2019 Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nat Biotechnol. Aug;37(8):907-915. doi:[10.1038/s41587-019-0201-4](https://doi.org/10.1038/s41587-019-0201-4).
+  * Kim, D., Paggi, J. M., Park, C., Bennett, C., & Salzberg, S. L. (2019). Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype. Nature biotechnology, 37(8), 907-915. doi:[10.1038/s41587-019-0201-4](https://doi.org/10.1038/s41587-019-0201-4).
 
 6. **samtools**:
-  * Li H., B. Handsaker, A. Wysoker, T. Fennell, J. Ruan, N. Homer, G. Marth, G. Abecasis, R. Durbin, and 1000 Genome Project Data Processing Subgroup. 2009. The Sequence alignment/map (SAM) format and SAMtools. Bioinformatics 25: 2078-9. doi:[10.1093/bioinformatics/btp352](http://dx.doi.org/10.1093/bioinformatics/btp352)
+  * Li, H., Handsaker, B., Wysoker, A., Fennell, T., Ruan, J., Homer, N., ... & Durbin, R. (2009). The sequence alignment/map format and SAMtools. Bioinformatics, 25(16), 2078-2079. doi:[10.1093/bioinformatics/btp352](http://dx.doi.org/10.1093/bioinformatics/btp352)
 
 7. **picard**:
   * “Picard Toolkit.” 2019. Broad Institute, GitHub Repository. [http://broadinstitute.github.io/picard/](http://broadinstitute.github.io/picard/); Broad Institute
 
 8. **featureCounts**:
-  * Liao, Y., Smyth, G.K., Shi, W. 2014 featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics. Apr 1;30(7):923-30. doi:[10.1093/bioinformatics/btt656](https://doi.org/10.1093/bioinformatics/btt656).
+  * Liao, Y., Smyth, G. K., & Shi, W. (2014). featureCounts: an efficient general purpose program for assigning sequence reads to genomic features. Bioinformatics, 30(7), 923-930. doi:[10.1093/bioinformatics/btt656](https://doi.org/10.1093/bioinformatics/btt656).
 
 9. **deeptools**:
-  * Ramírez, F., D. P. Ryan, B. Grüning, V. Bhardwaj, F. Kilpert, A. S. Richter, S. Heyne, F. Dündar, and T. Manke. 2016. deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic Acids Research 44: W160-165. doi:[10.1093/nar/gkw257](http://dx.doi.org/10.1093/nar/gkw257)
+  * Ramírez, F., Ryan, D. P., Grüning, B., Bhardwaj, V., Kilpert, F., Richter, A. S., ... & Manke, T. (2016). deepTools2: a next generation web server for deep-sequencing data analysis. Nucleic acids research, 44(W1), W160-W165. doi:[10.1093/nar/gkw257](http://dx.doi.org/10.1093/nar/gkw257)
 
 10. **Seqtk**:
   * Seqtk [https://github.com/lh3/seqtk](https://github.com/lh3/seqtk)
@@ -37,13 +37,13 @@
   * FastQC [https://www.bioinformatics.babraham.ac.uk/projects/fastqc/](https://www.bioinformatics.babraham.ac.uk/projects/fastqc/)
 
 13. **SeqWho**
-  * SeqWho [https://git.biohpc.swmed.edu/s181649/seqwho](https://git.biohpc.swmed.edu/s181649/seqwho)
+  * Bennett, C., Thornton, M., Park, C., Henry, G., Zhang, Y., Malladi, V. S., & Kim, D. (2021). SeqWho: Reliable, rapid determination of sequence file identity using k-mer frequencies. bioRxiv, 2021.2003.2010.434827. doi:[10.1101/2021.03.10.434827](https://doi.org/10.1101/2021.03.10.434827)
 
 14. **RSeQC**:
   * Wang, L., Wang, S., Li, W. 2012 RSeQC: quality control of RNA-seq experiments. Bioinformatics. Aug 15;28(16):2184-5. doi:[10.1093/bioinformatics/bts356](https://doi.org/10.1093/bioinformatics/bts356).
 
 15. **MultiQC**:
-  * Ewels P., Magnusson M., Lundin S. and Käller M. 2016. MultiQC: Summarize analysis results for multiple tools and samples in a single report. Bioinformatics 32(19): 3047–3048. doi:[10.1093/bioinformatics/btw354](https://dx.doi.org/10.1093/bioinformatics/btw354)
+  * Ewels, P., Magnusson, M., Lundin, S., & Käller, M. (2016). MultiQC: summarize analysis results for multiple tools and samples in a single report. Bioinformatics, 32(19), 3047-3048. doi:[10.1093/bioinformatics/btw354](https://dx.doi.org/10.1093/bioinformatics/btw354)
 
 16. **Nextflow**:
-  * Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., and Notredame, C. 2017. Nextflow enables reproducible computational workflows. Nature biotechnology, 35(4), 316.
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+  * Di Tommaso, P., Chatzou, M., Floden, E. W., Barja, P. P., Palumbo, E., & Notredame, C. (2017). Nextflow enables reproducible computational workflows. Nature biotechnology, 35(4), 316-319.
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