merqury vs Perfect-bacterial-genome-tutorial

merqury

k-mer based assembly evaluation (by marbl)

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Perfect-bacterial-genome-tutorial

By rrwick

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merqury		Perfect-bacterial-genome-tutorial
	Project
3	Mentions	2
258	Stars	104
6.6%	Growth	-
6.4	Activity	4.5
4 months ago	Latest Commit	2 months ago
Shell	Language	Python
GNU General Public License v3.0 or later	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.

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

Perfect-bacterial-genome-tutorial

Posts with mentions or reviews of Perfect-bacterial-genome-tutorial. We have used some of these posts to build our list of alternatives and similar projects. The last one was on 2023-01-10.

Bacterial WGS reads and assembly quality questions
3 projects | /r/bioinformatics | 10 Jan 2023

I have ONT and Illumina reads for a bacterial WGS (1.8 Mb) and I'm following Ryan Wick's methods for "perfect bacterial genome assembly" (https://github.com/rrwick/Perfect-bacterial-genome-tutorial). I've ran into a few questions I have not been able to find answers to. I'm a grad student struggling in a mostly clinical lab.
Is Unicycler the best option for hybrid genome assembly?
4 projects | /r/bioinformatics | 4 Oct 2022

You should read this https://github.com/rrwick/Perfect-bacterial-genome-tutorial

What are some alternatives?

When comparing merqury and Perfect-bacterial-genome-tutorial 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

ALE - Assembly Likelihood Estimator

EukRep - Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets

Scoary - Pan-genome wide association studies

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.