SISRS: SNP Identification from Short Read Sequences¶
SISRS — pronounced “scissors” — is a program for identifying phylogenetically informative sites from next-generation whole-genome sequencing of multiple species. It identifies homologous sites without the need to do de novo assembly, annotation, and alignment. It identifies conserved regions by doing joint de novo assembly on multiple species. Sequencing reads are then aligned back to the contigs to identify variable sites.
- Authors:
- This software is written by members of:
- Schwartz Lab @ URI
- The Developers:
- Dr. Rachel Schwartz (Original developer)
- Dr. Robert Literman
- Devin J. McConnell
Associated Publications¶
Publications are shown in revers chronological order:
- Literman, R. and R.S. Schwartz. 2019. Genome-scale profiling reveals higher proportions of phylogenetic signal in non-coding data. BioRxiv Preprint.
- Harkins, K.M., R.S. Schwartz, R.A. Cartwright, and A.C. Stone. 2016. Phylogenomic reconstruction supports supercontinent origins for Leishmania. Infection, Genetics and Evolution 38: 101-109.
- Schwartz, R.S., K.M Harkins, A.C. Stone, and R.A. Cartwright. 2015. A composite genome approach to identify phylogenetically informative data from next-generation sequencing. BMC Bioinformatics. 16:193.
Funding¶
This research was funded by a NSF grant DBI-1356548 to R. Cartwright, funding from URI, and a NSF postdoctoral fellowship to R. Literman.
Questions¶
We ask that all questions be asked on our github @ Schwartz Lab: SISRS