Quast Input scaffolds

I input two scaffolds files which I want to compare and again input two contigs files for another round. But the HTML report indicate contig amount in each time. So how would I determine the exact numbers of scaffolds and contigs. These contigs and scaffolds are outputs of same inputs.

Appreciate your help

Thank you

Welcome, @Vishmi_Abeyrathna

I’m not entirely clear on what your question is asking, so you could clarify a bit more if this reply does not help.

For scaffold inputs, try using these options:

  1. Tell the tool that the inputs are scaffolds with Are assemblies scaffolds rather than contigs? set to YES.

  2. To produce extended statistics, include Use a reference genome? as YES, and input the genome fasta file.

  3. Then, you can optionally toggle the option Report all metrics as YES.

The Quast manual describes what each do exactly, and there are other related options to fine tune how the scaffolds are handled.

We have many tutorials that incorporate this tool … maybe those will help too? See → Tutorials using iuc/quast

Let’s start there :slight_smile: