Assembly: Branching and Merging¶
Branching can be used to create a new assembly with a different name and to which you can apply new parameters and create new downstream files …
Merging can be used to combine samples from multiple libraries.
Drop samples by branching¶
Another point where branching is useful is for adding or dropping samples from an assembly, either to analyze a subset of samples separately from others, or to exclude samples with low coverage. The branching and merging fuctions in ipyrad make this easy. By requiring a branching process in order to drop samples from an assembly ipyrad inherently forces you to retain the parent assembly as a copy. This provides a nice fail safe so that you can mess around with your new branched assembly without affecting it’s pre-branched parent assembly.
Examples using the ipyrad CLI
## branch and only keep 3 samples from assembly data1
>>> ipyrad -n data1 -b data2 1A0 1B0 1C0
## and/or, branch and only exclude 3 samples from assembly data1
>>> ipyrad -n data1 -b data3 - 1A0 1B0 1C0
Examples using the ipyrad Python API
## branch and only keep 3 samples from assembly data1
>>> data1.branch("data2", subsamples=["1A0", "1B0", "1C0"])
## and/or, branch and only exclude 3 samples from assembly data1
>>> keep_list = [i for i in data1.samples.keys() if i not in ["1A0", "1B0", "1C0"]]
>>> data1.branch("data3", subsamples=keep_list)