Thank you for your suggestions @Eleftherios Bochalis and @Evangelos Karatzas. I am really happy to hear that there are people willing to contribute to the development of the pipeline. I agree that there is plenty of room for improvement to make it more useful. Because I started working on this pipeline as a part of my PhD project, I will just need to check with my supervisor about some things. I will aim get back to you about this in a few days

Looking forward to this! Let us know when, to coordinate efforts 😄 We can start with a roadmap, building in the smallest tweaks (i.e., couple of new complementary modules) and then moving to complementary subworkflows and methodologies, if possible.

Hi Eleftherios and Evangelos, I have spoken to my supervisors. Unfortunately, I won't be able to contribute to further development of the pipeline due to time constraints during my PhD. As it is an open-source tool, we're very happy for you to contribute. I am happy to join a call to give my perspective if it helps with planning. I also wanted to let you know that we have a manuscript about the pipeline which we are planning to publish, based on that the work that has been done up to v1.2.0. I'll just tag @Timothy Little here to keep him in the loop as he was involved with that. Let me know how you'd like to move forward 🙂

Thank you Avani! Yep, we'll start implementing some modules here and there, and if you find the time, you could potentially do some code reviews in the future 😉 Eleutherios us currently updating the pipeline schema with the changes we aim to implement, as a roadmap, and we will soon post it here so you can take a look. We can organise a call after this to have something concrete to talk upon!

sounds good!

Hello Avani! I have attached the updated pipeline schema with the annotation process, Also, I have added a step before Trinity that implements Jellyfish to find the optimal k-mer length for the assembly. Looking forward to hearing your thoughts on this!