Entering edit mode
7.0 years ago
martingarridorc
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20
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.
martingarridorc Why did you delete this post? Others have contributed to this post and deleting it would take away from the knowledge repository aspect of Biostars. Please let us know if you have a pressing concern about this post and the admin will remove it.