tomharrop / asw-annotate

asw-flye-withpool

Genome annotation for Argentine stem weevil, described in https://github.com/TomHarrop/asw-gbs-genome-paper.

Citation

Thomas W. R. Harrop, Marissa F. Le Lec, Ruy Jauregui, Shannon E. Taylor, Sarah N. Inwood, Tracey van Stijn, Hannah Henry, et al. 2020. “Genetic Diversity in Invasive Populations of Argentine Stem Weevil Associated with Adaptation to Biocontrol.” Insects 11 (7): 441. 10.3390/insects11070441.

Requirements

All software run in containers, so the only requirements are:

• singularity ≥ 3.5.3
• snakemake ≥ 5.9.1

Reproduce the analysis

snakemake --use-singularity

Input data files

• Raw reads are hosted at the NCBI SRA under accession PRJNA64051
• Annotation databases for emapper.py and interproscan.sh (eggnog_proteins.dmnd, PANTHER) have to be downloaded separately

Workflow