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First release of epiGBS2

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@FleurGaBru FleurGaBru released this 11 May 10:40
· 14 commits to epiGBS2 since this release
v1.0.0
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Learn about vigilant mode.

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

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