Question: Drosophila melanogaster assembly
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mgrcprof • 20 wrote:
Hi guys!
I have several questions;
1) Which assembler should I use in order to make a de novo assembly of Drosophila melanogaster WGS experiment? I'm not interested in the alignment vs the Ref Genome, I just want to generate the scaffolds/contigs.
2) Does exists an aligner that allows you to choose a MAXIMUM query coverage (yes, it's maximum, not minimum) ?
Thank you!
See several options: https://omictools.com/genome-assembly-category
It's important to state which data you have available for this assembly, for sure the read length.
I have paired-ends reads files (.fastq) each one with ~ 6 million reads with a 74 pb length.
That amount of data (900 Mbp) is only five-fold coverage of the 175 Mbp fly genome, which is insufficient for assembly.
It's SRA data, i can have several fastq of this type (6 exactly) until reaching a higher coverage. In this case, what assembler do i need to use? the SRA experiment: SRX078313.
I moved this to a comment because that's what it is.