Assembly quality check

Question

[tothepoint]

I am working on PacBio data and currently performing De novo assembly via Canu assembler. Currently I finished Polishing step using arrow algorithm and generated polished contigs .fasta file and .gff file. Now I am stuck at this step and not able to find suitable way to check the quality of polished contigs such as N50, L50 number of contigs, contigs length etc. And why after polishing step the contig file generated having more size than canu assembly having less size as what I able to understand is polishing remove error and size should decrease. Please show me a way to proceed. I am a newbie in assembly and need your help.

Answer 1

[hafiz.talhamalik]

Use quast