reference-guided denovo assembly
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3 months ago

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?

next-gen denovo stringTie Assembly genome assembl reference-guided • 217 views
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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).

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