Scoary
merqury
| Scoary | merqury | |
|---|---|---|
| 2 | 3 | |
| 137 | 262 | |
| - | 5.3% | |
| 10.0 | 5.5 | |
| over 1 year ago | 5 days ago | |
| Python | Shell | |
| GNU General Public License v3.0 only | GNU General Public License v3.0 or later |
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Scoary
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Functional pangenome analysis using Roary strategy?
How about mGWAS, such as Scoary or my about-to-be-published successor Scoary2?
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Is Unicycler the best option for hybrid genome assembly?
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?
merqury
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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?
plassembler - Program to quickly and accurately assemble plasmids in hybrid and long-only sequenced bacterial isolates
quast - Genome assembly evaluation tool
scoary-2 - Calculate assocations between genes and traits
EukCC - Tool to estimate genome quality of microbial eukaryotes
sgkit - We've moved to https://github.com/sgkit-dev/sgkit
EukRep - Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets
Perfect-bacterial-genome-tutorial
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.