This PR is really sad -- it's rips out all of the code that supported single end read processing along side paired end read processing. This is removed because:
Single end libraries produce more fragmented assemblies than paired end assemblies.
There is no way to evaluate single end libraries with transrate.
I'm glad this approach is recorded in the git history for this repo because I really like it for mixing se/pe reads. It was inspired by @ecpierce's chelicerate analysis Snakefile.
5 should be reviewed and merged before this PR is reviewed.
This PR is really sad -- it's rips out all of the code that supported single end read processing along side paired end read processing. This is removed because:
I'm glad this approach is recorded in the git history for this repo because I really like it for mixing se/pe reads. It was inspired by @ecpierce's chelicerate analysis Snakefile.
5 should be reviewed and merged before this PR is reviewed.