webseq is an R package for for working with biological sequence
databases. It interacts with web services to download biological
sequences or retrieve aditional information (metadata) about biological
sequences. It is tailored towards whole genome sequencing reads,
assembled genomes, metagenomes and associated metadata.
Currently webseq can interact with the following web services:
- NCBI: https://www.ncbi.nlm.nih.gov/
- ENA: https://www.ebi.ac.uk/ena/browser/home
- MGnify: https://www.ebi.ac.uk/metagenomics
The package is under development, some of the functionality may be very limited at this point.
install.packages("devtools")
devtools::install_github("stitam/webseq")To cite webseq in publications use:
Stirling T (2024). webseq: Tools for working with biological sequence databases in R. https://zenodo.org/doi/10.5281/zenodo.10521754