I am planning to conduct de novo assembly of a bumblebee species and it is haploid. I was wondering what assembler would be best for it? I am considering platanus, megahit and hapsembler at this moment.
The assembly depends on research question. Why would you try a denovo assembly with just a single illumina library when you already have such a good genome as suggested by Philipp? If you are trying a reference-based assembly MIRA would be a good start.
The whole assembly pipeline would depend on what kind of data you have - coverage and quality are the prime factors to consider. Since you have 150 bp illumina, you would have to go for de-brujin assemblers that can handle multiple libraries. Paired-end overlap would be the first thing to do since your insert size is low, this should be supplied as another single-end library. All you would get in the end would be various many contigs broken at repetitive or high complexity regions.
Without multiple libraries or sequencing technologies, you would get highly fragmented assemblies - Is this what you need?
I went with MIRA and experimented with several parameters. I got a assembly which had N50 value of 50KB and blast results provided the contigs for the region I am interested in. Thanks all for your help!