Dear all,
Earlier, I asked whether it is possible to denovo assemble a genome with 2.6 Gigabases by 130 GB RAM from Illumina reads with 10X coverage. I realized, both the coverage and my RAM are not enough for denovo assembly. Recently, I have come across some papers that use a reference genome from a close species and do reference-guided denovo assembly. For example, see the following paper: https://doi.org/10.1186/s12859-017-1911-6. As far as I know, StringTie is a program for reference-guided denovo assembly of the transcriptome, and it needs a bam file as input. I wondered whether I could map my reads to a reference genome from a close species (by bowtie2) and then use StringTie for reference-guided denovo assembly of the genome (rather than transcriptome)? Will it work for my case?
There are other programs for reference guide assembly (Reference guided assembly methods and Reference Guided De Novo assembly of Contigs generated from Illumina PE Reads ) but you are likely to run into the same issue (not enough RAM).