Update README.md

README.md

@@ -81,6 +81,10 @@ Please also cite the read mapper you selected.
 
 > Langmead B, Salzberg SL (2012). "Fast gapped-read alignment with Bowtie 2." *Nat Methods*. 9(4):357-359. [doi:10.1038/nmeth.1923](https://doi.org/10.1038/nmeth.1923)
 
+* DRAGMAP
+
+> https://github.com/Illumina/DRAGMAP
+
 * HISAT2
 
 > Kim D, Paggi JM, Park C, Bennett C, Salzberg SL (2019). "Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype." *Nat Biotechnol*. 37:907-915. [doi:10.1038/s41587-019-0201-4](https://doi.org/10.1038/s41587-019-0201-4)
@@ -89,6 +93,10 @@ Please also cite the read mapper you selected.
 
 > Ren J, Chaisson MJP (2021). "lra: A long read aligner for sequences and contigs." *PLoS Comput Biol*. 17(6):e1009078. [doi:10.1371/journal.pcbi.1009078](https://doi.org/10.1371/journal.pcbi.1009078)
 
+* NGMLR
+
+> Sedlazeck FJ, Rescheneder P, Smolka M, Fang H, Nattestad M, von Haeseler A, Schatz MC (2018). "Accurate detection of complex structural variations using single-molecule sequencing." *Nat Methods*. 15:461-468. [doi:10.1038/s41592-018-0001-7](https://doi.org/10.1038/s41592-018-0001-7)
+
 * STAR
 
 > Dobin A, Davis CA, Schlesinger F, Drehkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR (2013). "STAR: ultrafast universal RNA-seq aligner." *Bioinformatics*. 29(1):15-21. [doi:10.1093/bioinformatics/bts635](https://doi.org/10.1093/bioinformatics/bts635)
@@ -97,6 +105,10 @@ Please also cite the read mapper you selected.
 
 > Li H (2021). "Unimap: A fork of minimap2 optimized for assembly-to-reference alignment." https://github.com/lh3/unimap
 
+* wfmash
+
+> Jain C, Koren S, Dilthey A, Phillippy AM, Aluru S (2018). "A Fast Adaptive Algorithm for Computing Whole-Genome Homology Maps". *Bioinformatics*. 34(17):i748-i756. [doi:10.1093/bioinformatics/bty597](https://doi.org/10.1093/bioinformatics/bty597)
+
 # Common Issues
 ## Weird ViralMSA output on sequences with many `N`s
 It seems as though, in some cases in which an input viral sequence has many `N`s within the sequence, Minimap2 splits the input sequence at each long consecutive chain of `N`s and produces an alignment for each fragment of the input sequence, with only one of these alignments (probably the longest one?) being labeled as the primary alignment (flag 0 in the SAM file) and all others being labeled as supplementary alignments (flag 2048 in the SAM file). This issue should be fixed in [ViralMSA 1.1.12](https://github.com/niemasd/ViralMSA/releases/tag/1.1.12), but if you run into this issue, a simple fix that seems to work well is to simply shorten the streches of `N`s in the sequence to be at most ~100 before running ViralMSA.