merqury vs Scoary

merqury

k-mer based assembly evaluation (by marbl)

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Scoary

Pan-genome wide association studies (by AdmiralenOla)

gene-presence-absence Gwas pan-genome bacteria Genomics

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merqury		Scoary
	Project
3	Mentions	2
258	Stars	137
6.6%	Growth	-
6.4	Activity	10.0
4 months ago	Latest Commit	over 1 year ago
Shell	Language	Python
GNU General Public License v3.0 or later	License	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.

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.

which tool is recommended for kmer based analysis to compare draft genome and sequencing reads.
2 projects | /r/bioinformatics | 28 Mar 2023

KAT or merqury. Avoid QUAST.
Is Unicycler the best option for hybrid genome assembly?
4 projects | /r/bioinformatics | 4 Oct 2022

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.
Deciding on genome assembly software
6 projects | /r/bioinformatics | 1 Oct 2021

I would recommend using Merqury to see the completeness and quality of your assembly. https://github.com/marbl/merqury

Scoary

Posts with mentions or reviews of Scoary. We have used some of these posts to build our list of alternatives and similar projects. The last one was on 2022-11-28.

Functional pangenome analysis using Roary strategy?
2 projects | /r/bioinformatics | 28 Nov 2022

How about mGWAS, such as Scoary or my about-to-be-published successor Scoary2?
Is Unicycler the best option for hybrid genome assembly?
4 projects | /r/bioinformatics | 4 Oct 2022

BONUS: I was planning on using Scoary (https://github.com/AdmiralenOla/Scoary) together with some Virulence data I have to look for some candidates. Any suggestion of alternative ways to identify virulence factors in these genomes?

What are some alternatives?

When comparing merqury and Scoary you can also consider the following projects:

quast - Genome assembly evaluation tool

plassembler - Program to quickly and accurately assemble plasmids in hybrid and long-only sequenced bacterial isolates

EukCC - Tool to estimate genome quality of microbial eukaryotes

scoary-2 - Calculate assocations between genes and traits

EukRep - Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets

sgkit - We've moved to https://github.com/sgkit-dev/sgkit

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

Perfect-bacterial-genome-tutorial

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.