resources
List of research resources developed by Fukushima lab
GitHub Repositories
Genomes
| Species | NCBI Genome | CoGe (OrganismView for genome browser) | Publication |
|---|---|---|---|
| Cephalotus follicularis | GCA_001972305.1 | 29002 | Fukushima et al. (2017) |
| Nepenthes gracilis | GCA_033239525.1 | 61566 | Saul et al. (2023) |
Internal Resources
kflab
This repository is designed as the primary platform for coordinating laboratory activities within the Kenji Fukushima lab. Our focus here extends beyond programming code, encompassing a broad spectrum of discussions relevant to our research. These include logistics like lab supply management, strategic considerations in experimental design, and updates on research progress. New members should create a GitHub account and request an invitation from Kenji Fukushima.
gfe_pipeline
gfe_pipeline is an in-house tool that was originally developed for analyzing gene family evolution using an in-house Apptainer/Singularity container, gfe. Currently, gfe_pipeline has expanded to include many bioinformatics tools beyond gene family analysis. These include transcriptome assembly, gene annotation, species tree inference, SNV analysis, synteny analysis, and more. For example, a significant portion of the data presented in the studies by Fukushima & Pollock (2020), Fukushima & Pollock (2023), and Saul et al. (2023) was generated using the gfe_pipeline. Lab members who wish to obtain access rights should make a request to Kenji Fukushima.