pestalotiopsis
Assembly and phylogentic analysis pipeline for draft genome of a Pestalotiopsis fungi. (by EverymanBio)
Flye
De novo assembler for single molecule sequencing reads using repeat graphs (by fenderglass)
| pestalotiopsis | Flye | |
|---|---|---|
| 1 | 4 | |
| 7 | 730 | |
| - | - | |
| 0.0 | 4.7 | |
| about 2 years ago | about 2 months ago | |
| Python | C | |
| GNU General Public License v3.0 only | GNU General Public License v3.0 or later |
The number of mentions indicates the total number of mentions that we've tracked plus the number of user suggested alternatives.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
Stars - the number of stars that a project has on GitHub. Growth - month over month growth in stars.
Activity is a relative number indicating how actively a project is being developed. Recent commits have higher weight than older ones.
For example, an activity of 9.0 indicates that a project is amongst the top 10% of the most actively developed projects that we are tracking.
pestalotiopsis
Posts with mentions or reviews of pestalotiopsis.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2021-12-26.
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Sequencing your DNA with a USB dongle and open source code
That's not true. I just did a high-quality sequence and assembly of a new species of fungus from my home lab using nanopore. You can see all my code used for assembly and analysis that will be referenced in a paper I plan to publish in Jan here: https://github.com/EverymanBio/pestalotiopsis
Flye
Posts with mentions or reviews of Flye.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2021-12-26.
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Anyone with bioinformatics experience to offer advice?
My crash cores in trying to figure your use case out turned up a few things (1 2):
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What is the best approach to building a genome when the Reference sequence is not available?
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.
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Sequencing your DNA with a USB dongle and open source code
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?
What are some alternatives?
When comparing pestalotiopsis and Flye you can also consider the following projects:
malware-phylogeny - malware phylogeny for WSO web shell, Shellbot IRC bot and algorithm