merqury
k-mer based assembly evaluation (by marbl)
EukRep
Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets (by patrickwest)
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| merqury | EukRep | |
|---|---|---|
| 3 | 1 | |
| 258 | 62 | |
| 6.6% | - | |
| 6.4 | 0.0 | |
| 4 months ago | over 2 years ago | |
| Shell | Python | |
| GNU General Public License v3.0 or later | MIT License |
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
EukRep
Posts with mentions or reviews of EukRep.
We have used some of these posts to build our list of alternatives
and similar projects. The last one was on 2021-10-01.
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Deciding on genome assembly software
Have you looked into QUAST for comparison of assemblies? How big is the bacterial community? You may need to do some binning of your contigs to separate them into species specific genomes. I can suggest metaGEM (developed by me! should be online in NAR any day now) for generating MAGs for your bacterial species. Although it currently only supports short reads, it may give you an idea of what the bacterial community looks like. Maybe also look into EukCC for estimating fungal genome completeness and/or EukRep for splitting the contigs according to prokaryotic/eukaryotic provenance. You could also try estimating community composition directly from short read analysis using e.g. mOTUs2, kraken/braken, metaphlan, etc.
What are some alternatives?
When comparing merqury and EukRep you can also consider the following projects:
quast - Genome assembly evaluation tool
EukCC - Tool to estimate genome quality of microbial eukaryotes
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
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.