Resources

Funders

National Science Foundation
National Institute of General Medical Sciences
National Institute of Allergy and Infectious Disease

Short Read Data archives

Warrier, Ram Mohan, et al. PLoS Pathogens 2018

• SRP136114
• PRJNA609728

Pei et al. BMC Genomics 2017

• SRP077756

Custom Scripts and Software Packages

Eichelman and Meyer BioRxiv 2024

• Custom python scripts.

Furumo and Meyer BMC Bioinformatics 2024

• https://bioconductor.org/packages/release/bioc/html/PIPETS.html
• https://github.com/qfurumo/PIPETS

Crumm et al. PLOS Comp. Biol. 2019

• https://github.com/mcrum8/Riboswitch_Basic_Graph_Clustering

Warrier, Ram Mohan, et al. PLOS Path. 2018

• https://github.com/nikhilram/T4pipeline

Pei et al. BMC Bioinformatics

• https://github.com/ship561/hts-exploration.

Other useful resources

• RNAcentral – The noncoding RNA sequence database
• Rfam – RNA families database
• NCBI Microbial Genomes