romainferon / paper-sexdetermination-bowfin

Workflow and scripts used for sex determination analyses in Bowfin

Scripts used in the analyses of sex determination for Bowfin

Analyses were run by Qiaowei Pan with input from Romain Feron for the bowfin genome paper paper (update after pub).

Reference-based pooled sequencing analyses

The PSASS snakemake workflow was run using the config file config.yaml provided in psass/. The workflow itself is provided in psass/ and can be run with snakemake >= 5.8.1 with the --use-conda flag.

Sex-biased kmer analyses

Scripts used to identify sex-biased kmers are provided in kpool/; they require Jellyfish 2.2.10 and Kpool. Scripts were run in the following order:

• jelly_count_female.sh
• jelly_count_male.sh
• jellyfish_dump_female.sh
• jellyfish_dump_male.sh
• merge_table.sh
• filter_table.sh

Generate basic figure

Data and an R script to generate the base figure included in the paper are provided in figure. You only need to replace the folder path with that of the figure folder in the R script to replicate the figure.