How other assemblers tools with 4CAC #4
Description
Hello author, I appreciate your effort in developing such a user-friendly classification tool ---“4CAC”https://github.com/Shamir-Lab/4CAC.
When compared to SPAdes, MEGAHIT exhibits lower memory consumption, whereas penguin demonstrates superior performance in virus assembly tasks.
Based on my current understanding, all three tools are grounded in the De Bruijn graph assembler agorithm. Nonetheless, it appears that MEGAHIT and penguin do not directly produce gfa or path information. Given my limited expertise in this area, could you kindly examine this matter? If feasible, it would significantly aid my research endeavors.
Below, I've included information pertaining to MEGAHIT and penguin.
MEGAHIT ：https://github.com/voutcn/megahit
Li, D., Liu, C-M., Luo, R., Sadakane, K., and Lam, T-W., (2015) MEGAHIT: An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics, doi: 10.1093/bioinformatics/btv033
penguin ：https://github.com/soedinglab/plass
Jochheim A, Jochheim FA, Kolodyazhnaya A, Morice É, Steinegger M, Söding J. Strain-resolved de-novo metagenomic assembly of viral genomes and microbial 16S rRNAs. Microbiome. 2024;12(1). doi:10.1186/s40168-024-01904-y