Shortest scaffold

Question

[Takuma]

Using Platanus, I did genome assembly for a non-model insect.

After exculding contigs below 500 bp, I performed scaffolding. But the shortest scaffold was about 400 bp. I am wondering why the shortest scaffold was smaller than 500 bp. In other words, do you have any idea abot the condition that the shortest scaffold is smaller than the shortest contig ?

Plesase let me know.

Answer 1

[Istvan Albert]

Assemblers are complex pieces of software with dozens upon dozens of filtering and correction steps and can produce seemingly counterintuitive results

When you apply various filters, the order of operation can produce unexpected results.

Say you merge contigs first but later only trust regions covered by at least two reads. Now if only two reads happen to overlap then only the overlapping region is "trustworthy," and the resulting assembly is shorter than each of the inputs.

So I would not worry about it and filter the results yet again.

[Takuma]

Dr Albert, thank you for helpful comment. At last I have solved the puzzle.