How to evaluate an assembly

VirAmp uses QUAST (Quality Assessment Tools for Genome Assemblies) to evaluate the newly assembled genome.

Basic statistics such as contig lengths, N50, NG50, # misassemblies etc. are given on screen, and more detailed report is provided for download on the right "history" panel.

Two important statistics here are N50 and NG50.

• N50 is a weighted median statistic such that 50% of the entire assembly is contained in contigs or scaffolds equal to or larger than this value (Rounsley, S. etc. 2009). This is one of the most accepted statistics to evaluate the quality of assembly.
• NG50 is a modified version of N50. When a reference genome is presented, the length of reference genome is used for normalization instead of the cumulative length of the entire assembly. This reduces the bias brought by misassemlies, which may cause trouble when the percentage of misassemblies is significant.

What to input

1. Reference genome in FASTA format
2. Target genome: Your newly assembled genome (or other genome you want to compare with the referece) in FASTA format
3. Contig length threshold: Minimum length of contigs you want to consider as valid, by default is 500 nucleotides.

• What is shown on screen:

  Assembly                   viramp
  # contigs (>= 0 bp)        5
  # contigs (>= 1000 bp)     5
  Total length (>= 0 bp)     135722
  Total length (>= 1000 bp)  135722
  # contigs                  5
  Largest contig             108094
  Total length               135722
  Reference length           136376
  GC (%)                     67.36
  Reference GC (%)           67.53
  N50                        108094
  NG50                       108094
  N75                        108094
  NG75                       108094
  # misassemblies            0
  # local misassemblies      3
  # unaligned contigs        0 + 1 part
  Unaligned contigs length   95
  Genome fraction (%)        98.610
  Duplication ratio          1.009
  # N's per 100 kbp          106.84
  # mismatches per 100 kbp   472.19
  # indels per 100 kbp       72.87
  Largest alignment          107807
  NA50                       107807
  NGA50                      107807
  NA75                       107807
  NGA75                      107807
  

Featured graphs in the download version

Reference

QUAST: quality assessment tool for genome assemblies. Alexey Gurevich, Vladislav Saveliev, Nikolay Vyahhi and Glenn Tesler. Bioinformatics (2013)29(8):1072-1075.