Implementation of single end reads

algbioi / snowball

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Implementation of single end reads #3

Open jregalad opened 7 years ago

jregalad commented 7 years ago

Is there any plans to include the addition of single end reads? I have several paired end libraries and additional single end libraries of the same metagenomes. It will be nice to see how your algorithm performs with this additional data.

It is also often the case where paired-end libraries are generated from different machines eg: HiSeq (read length 2x150bp) and MiSeq (2x250). so far all reads provided to snowball have to be of the same length which is quite inconvenient.

algbioi commented 7 years ago

Thank you very much for your feedback, it is valuable for us. I agree that it definitely makes sense to support single-end reads. Our plan is to first collect feedback and then decide what to do next with Snowball.

algbioi commented 7 years ago

Concerning the SE reads, I implemented an experimental script to preprocess the input, it's described here: https://github.com/algbioi/snowball/commit/3e34821b0679bb31743b8b353a201ff9a98fee90