epiGBS2v3.1

• Improved performance of clone_filter by using a newer version of stacks
• Added polyG problem and clone_filter memory issues to the error section of the readme

epiGBS2 release with some bug fixes

src/rules/denovo.rules:

• library is now always directional
• to save space, six output files were made temporary

src/rules/reference.rules:

• library is now always directional
• to save space, six output files were made temporary
• added flag “—scaffolds” during methylation calling to allow compatibility with reference genome assemblies with contigs
• removed MQ parameter in rule SNP calling

src/env/bismark.yaml :

• fixed problems with the environment files

src/parameter_test/paramTest.tsv :

• improved default parameters

src/rules/paramTest.rules:

• fixed bugs

epiGBS2 release with Bismark and Freebayes

This release includes several major changes:

• usage of Bismark for mapping and methylation calling
• usage of Freebayes for SNP calling
• creation of a report file using multiQC
• split conda environments
• compatibility with snakemake 6.1.1

First release of epiGBS2

This is the first realease of epiGBS2. It is an update of the software described in van Gurp et al. (2016, https://doi.org/10.1038/nmeth.3763).

• software is now integrated with conda and snakemake

• execution and error handling is documented

• the demultiplexing is increased in speed and is executed by stacks

• mapping is done by STAR

• variant calling is performed by samtools mpileup

• methylation calling and SNP calling is done by customised scripts

• report files for quality checks are added

• several minor bug-fixes

• pipeline has to be benchmarked in more detail