naturalis/brassica-snps

Refining Bulk Segregant Analyses: Ontology-Mediated Discovery of Flowering Time Genes in Brassica oleracea

Description

This repository contains the code for performing the GO-mediated refinement of BSA results as described in 10.1101/2021.08.11.455982. The repository's organization is inspired by the guidelines of 10.1371/journal.pcbi.1000424 and the preferred project layouts promulgated by the Perl5 community and is therefore intended to be understandable and reusable. Nevertheless, additional documentation has been added to the subfolders in this repository to further explain the various moving parts.

conf - configuration files for BioMart mappings and Circos plots
doc - documentation
lib - library code for object-relational mapping
results - intermediate and final output files
script - analysis scripts in Shell, Perl and R
sql - scripts for creating and managing database in Shell, Perl and SQL

How to use

The contents of this repository (scripts, library code) are meant to be used in conjunction with a fixed folder structure of input and reference data. The supplementary data files of the paper that describes our methods may serve as a template. Alternatively, the following structure may be replicated:

root ($DATA)
|-- reference (data: https://zenodo.org/record/3402201/files/reference.zip)
|-- BSA 
|   |-- $SAMPLE1 (contains FASTQ reads, e.g. https://www.ncbi.nlm.nih.gov/bioproject/PRJNA564368)
|   |-- $SAMPLE2
|   |-- $SAMPLE3
|   `-- $SAMPLE4
|-- contrasts
|   |-- $CONTRAST1 (will contain outputs)
|   |-- $CONTRAST2
|   |-- $CONTRAST3
|   |-- $CONTRAST4
|   |-- $CONTRAST5
|   `-- $CONTRAST6
`-- sqlite (contains chromosomes.tsv, e.g.: https://zenodo.org/record/3402201/files/sqlite.zip)

Note in this structure, the root folder can have any name, as long as this is specified as the value of the $DATA environment variable. Likewise, the samples and contrasts can have any name. In our analysis, they were labelled SAMPLE1=group-1-EF, SAMPLE2=group-2-IF, SAMPLE3=group-3-LF and SAMPLE4=group-5-NF but this can be anything reasonable. For the contrasts, we use CONTRAST1=EF-IF, CONTRAST2=EF-LF, CONTRAST3=EF-NF, CONTRAST4=IF-LF, CONTRAST5=IF-NF and CONTRAST6=LF-NF. As always, it is advisable to avoid special characters (such as directory separator symbols) and spaces in folder names.

With the above structure in place, the analysis steps as described in the supplementary methods PDF can be performed. Where applicable, the PDF indicates how various variables need to be updated for this to work with other file naming schemes than we followed.

We provide a Docker container inside of which are all the tools and their dependencies for running the analysis steps. That container should be run in interactive mode (i.e. the user 'boots into' the container to run a shell session). Additionally, the container must be made aware of the location of the above folder structure on the host machine such that it mounts it under /home/ubuntu/data inside the container. The command to start the container should therefore be something like:

docker run -it -v $DATA:/home/ubuntu/data naturalis/brassica-snps

Where $DATA is the absolute location of the root of the data folder on the host machine.

License

MIT License

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.