search

apetkau / core-phylogenomics

Pipeline for identifying core SNPs and building a phylogenetic tree
4 stars 4 forks source link

Calling SNPs on non-fastq files #16

Open nknox opened 9 years ago

nknox commented 9 years ago

When users want to included genomes for which they do not have access to fastq files - the current pipeline runs nucmer (pair-wise alignment) and calls SNPs using mummer. Ideally, reads should be simulated and FreeBayes/mpileup used to call variants.

apetkau commented 9 years ago

I agree that this would be a good way to go. Another good idea for a project.

For some of these components, I'd like to see them implemented as separate modules in a separate git repository. That we it makes integration into Galaxy a bit easier (we can include the Galaxy tool definition files) and gives a bit more separation.