Question: Drosophila melanogaster assembly
1
gravatar for martingarridorc
3.5 years ago by
Spain/Cordoba/IMIBIC
martingarridorc20 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!

assembly alignment wgs • 1.3k views
ADD COMMENTlink modified 3.5 years ago • written 3.5 years ago by martingarridorc20
1

See several options: https://omictools.com/genome-assembly-category

ADD REPLYlink written 3.5 years ago by genomax89k
1

It's important to state which data you have available for this assembly, for sure the read length.

ADD REPLYlink written 3.5 years ago by WouterDeCoster44k

I have paired-ends reads files (.fastq) each one with ~ 6 million reads with a 74 pb length.

ADD REPLYlink written 3.5 years ago by martingarridorc20
2

That amount of data (900 Mbp) is only five-fold coverage of the 175 Mbp fly genome, which is insufficient for assembly.

ADD REPLYlink written 3.5 years ago by harold.smith.tarheel4.6k

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.

ADD REPLYlink written 3.5 years ago by martingarridorc20

I moved this to a comment because that's what it is.

ADD REPLYlink written 3.5 years ago by WouterDeCoster44k
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