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Assess Quality of Assemblies with QUAST - v4.4
kb_quast

v.0.0.6

By: gaprice

Launch

Run QUAST (QUality ASsessment Tool) on a set of Assemblies to assess their quality.

This is the KBase wrapper for version 4.4 of the QUAST assembly quality assessment tool. QUAST evaluates assemblies by computing various metrics, including number of contigs, N50/75, L50/75, GC content, number of uncalled bases (N s), and predicted genes. It takes one or more Assembly objects as input and then generates an output report with statistics for all of the input assemblies.

Use QUAST to assess the output assemblies from different configurations of the same assembler, or compare assemblies from multiple assemblers to determine which one is optimal for downstream analysis. The QUAST report color codes "worst, median, best" for each of the statistics generated, but pay attention to the degree of difference between the lengths and values to better understand how the parameters of your assembler relate to the resulting Assembly.

Reading the QUAST output report:

Related Publications

  • [1] Gurevich A, Saveliev V, Vyahhi N, Tesler G. QUAST: quality assessment tool for genome assemblies. Bioinformatics. 2013;29: 1072 1075. doi:10.1093/bioinformatics/btt086 , https://www.ncbi.nlm.nih.gov/pubmed/23422339
  • [2] Mikheenko A, Valin G, Prjibelski A, Saveliev V, Gurevich A. Icarus: visualizer for de novo assembly evaluation. Bioinformatics. 2016;32: 3321 3323. doi:10.1093/bioinformatics/btw379 , https://www.ncbi.nlm.nih.gov/pubmed/27378299