plassembler
Program to quickly and accurately assemble plasmids in hybrid and long-only sequenced bacterial isolates (by gbouras13)
merqury
k-mer based assembly evaluation (by marbl)
plassembler | merqury | |
---|---|---|
2 | 3 | |
48 | 261 | |
- | 5.0% | |
8.8 | 6.4 | |
18 days ago | 4 months ago | |
Python | Shell | |
MIT License | 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.
plassembler
Posts with mentions or reviews of plassembler.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-01-10.
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Bacterial WGS reads and assembly quality questions
All looks pretty good to me, 1 is good and expected - circularised chromosome is great - and 2/3 is pretty normal - peak at >10x just because it includes 10-49x in the same histogram bin together, and the first few bases of the illumina read often jump around randomly until it settles down to approximqtely the gc content. Maybe run fastp on those short reads if you are concerned with the first bases. With 4 I’d run a webblast of some chunks of the assembly on nr to see if it’s close to anything/related species or strains (maybe not useful if this is a completely novel species). Also the polisher you used (eg polypolish) should tell you how many changes it made somewhere - if it’s many thousands then you might have a problem of the long and short reads not matching well (maybe if from different extractions), maybe try something like this https://github.com/gbouras13/plassembler (my own tool so self plug) to see if the long and short read sets match well. Another thing to try would be running the assembly through an annotation program like bakta - you would hope to see a high coding density and lots of well annotated cds. All in all what youve done looks pretty great to be honest, Ryan Wick’s tutorials are the bible so you’re already reading the right thing. Here’s the preprint too in case you havent read it https://preprints.scielo.org/index.php/scielo/preprint/view/5053
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Is Unicycler the best option for hybrid genome assembly?
And a bit of a self plug, but you want to look at getting plasmids try this (it’s a work in progress but hopefully should work) https://github.com/gbouras13/plassembler
merqury
Posts with mentions or reviews of merqury.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2023-03-28.
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which tool is recommended for kmer based analysis to compare draft genome and sequencing reads.
KAT or merqury. Avoid QUAST.
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Is Unicycler the best option for hybrid genome assembly?
Yeah, Unicycler is solid. iirc Unicycler v5.0+ removes Pilon, so you'll still want to polish your final assembly with your short reads. I like using QV as a quick way to see if I should polish more or not.
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Deciding on genome assembly software
I would recommend using Merqury to see the completeness and quality of your assembly. https://github.com/marbl/merqury
What are some alternatives?
When comparing plassembler and merqury you can also consider the following projects:
Scoary - Pan-genome wide association studies
quast - Genome assembly evaluation tool
Perfect-bacterial-genome-tutorial
EukCC - Tool to estimate genome quality of microbial eukaryotes
ALE - Assembly Likelihood Estimator
EukRep - Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets
metaGEM - :gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
CompareGenomeQualities - Reference free comparison of genome assemblies
KAT - The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra.