Flye Alternatives

Flye reviews and mentions

• Anyone with bioinformatics experience to offer advice?
  1 project | /r/PcMasterRaceBuilds | 20 Apr 2023

  My crash cores in trying to figure your use case out turned up a few things (1 2):

• What is the best approach to building a genome when the Reference sequence is not available?
  1 project | /r/bioinformatics | 4 Oct 2022

  As others have said, you are looking for de novo assembly. One thing to note is that short read assemblers like spades and megabit don't work great with long reads. I would use flye for those. After that you still need to annotate it but this depends on the organism.

• Sequencing your DNA with a USB dongle and open source code
  3 projects | news.ycombinator.com | 26 Dec 2021

  You totally should, it's a lot of fun. I'd suggest trying to find some bacterial genome sequencing (like E. coli) done on nanopore if you're interested in those data. I don't have a link to any handy right now, otherwise I'd post here, but assembling bacterial genomes is shockingly easy these days and doesn't need near as many resources as doing a human genome, so it's great for learning (I love the assembler Flye [1] for this).

  And RE: home sequencing, honestly the hardest part for a beginner will likely be the sample prep, since that takes some combination of wet lab experience and expensive equipment. I really wish molecular biology was as simple to get hacking on as writing software. The lag time between doing an experiment and getting a result is so much longer than waiting for things to compile, it just makes improving your skills take longer.

  [1] https://github.com/fenderglass/Flye

• Which one is a more convenient assembly?
  1 project | /r/bioinformatics | 20 Dec 2020
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