merqury
k-mer based assembly evaluation (by marbl)
CompareGenomeQualities
Reference free comparison of genome assemblies (by wurmlab)
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| merqury | CompareGenomeQualities | |
|---|---|---|
| 3 | 1 | |
| 258 | 5 | |
| 6.6% | - | |
| 6.4 | 0.0 | |
| 4 months ago | almost 3 years ago | |
| Shell | Shell | |
| GNU General Public License v3.0 or later | GNU General Public License v3.0 only |
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.
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
CompareGenomeQualities
Posts with mentions or reviews of CompareGenomeQualities.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2021-10-01.
-
Deciding on genome assembly software
Our tool: https://github.com/wurmlab/CompareGenomeQualities tries to rank assemblies by balancing different types of biologically relevant information
What are some alternatives?
When comparing merqury and CompareGenomeQualities you can also consider the following projects:
quast - Genome assembly evaluation tool
EukCC - Tool to estimate genome quality of microbial eukaryotes
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
Scoary - Pan-genome wide association studies
KAT - The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra.