Bioinformatics resources and best-practices for plant breeders

This material is maintained by Najla Ksouri, Chesco Montardit, Ernesto Igartua, Ricardo Ramírez González, Bruno Contreras Moreira and the Ensembl outreach team

Summary

Here we review some bioinformatics resources and databases which can be useful in plant breeding and genomics. We will use both standalone and Web-based tools and will also review reproducible analysis practices and software benchmarks. Test data used in sessions 1-4 can be obtained from https://github.com/eead-csic-compbio/bioinformatics.

Docker image

A Docker image is available with most of the software used in the sessions, excluding R, which we expect to be installed elsewhere. After installing Docker, it can be run as follows, note that you might require sudo:

docker pull csicunam/bioinformatics_iamz

# persistent folder for results files
mkdir $HOME/vep_data 
chmod a+w $HOME/vep_data

sudo docker run -t -i -v $HOME/vep_data:/data -v /tmp/.X11-unix:/tmp/.X11-unix -e DISPLAY=$DISPLAY csicunam/bioinformatics_iamz:latest

Contents

session	title	required time	URL
1	Annotation of coding sequences	4h	session 1
2	Analysis of non-coding sequences	4h	session 2
3	Reproducible analysis practices	2h	session 3
4	Benchmarks	2h	session 4
5	Mapping, variant calling & effect prediction	6h	session 5 , session 5a
6	Genotyping	3h	session 6
7	Genome-Wide Association Analysis	2h	session 7

We post regularly about these and related bioinformatics topics at the #!/perl/bioinfo blog, mostly in Spanish.

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