I have sequenced the complete genome of a plant species using two technologies
The estimated genome size using flowcytometer is estimated to be 300Mb
1. Illumina(mate pair)
2. Oxford Nanopore (for long reads which helps in the process of scafolding)
Therfore can anybody suggest the best tools for denovo genome assemblers for plant species
For hybrid assemblies, DBG2OLC has been reported to have good results.
https://github.com/yechengxi/DBG2OLC
Ye, Chengxi, et al. "DBG2OLC: efficient assembly of large genomes using long erroneous reads of the third generation sequencing technologies."Scientific reports 6 (2016): 31900.
Also, from version 3.0, the popular SPAdes assembler supports hydrid assembly too:
http://cab.spbu.ru/software/spades/
Consider a server with at least 512GB of main memory (RAM). I hope that helps. Best regards.
There is no "best" assembler, as each one might be more appropriate for a given dataset, platforms, coverage, error-rate, etc. Additionally, is is always interesting try different programs, with different configurations (ex: k-mers sizes), and them generate a consensus assembly using some assembly reconciliation tool (ex: CISA, MAIA, Mix). However, in your case i would just SPAdes, the Celera Assembly and MIRA, followed by a assembly integration using CISA and scaffolding and gap-closing procedures using tools such as SGA (scaffolding using illumina data), GMCloser (gap closing).
Oxford nanopore has a pipeline for hybrid assembly that uses illumina reads for polishing your nano pore data. It uses Canu (former Celera assembler, Racon to polish the illumina reads and pilion to correct the contigs. Here is the link, I think is a good pipeline.
https://nanoporetech.com/resource-centre/publications/hybrid-assembly-pipeline-released-using-canu-racon-and-pilon
I read the above comments but SPADES, MISA etc designed for smaller genomes, not for plants having more than 100MB genome. Did you found one ?
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