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:
- # contigs is the total number of contigs in the Assembly.
- Largest contig is the length of the longest contig in the Assembly.
- Total length is the total number of bases in the Assembly.
- GC (%) is the total number of G and C nucleotides in the Assembly, divided by the total length of the Assembly.
- N50 is the length for which the collection of all contigs of that length or longer covers at least half (50%) the total base content of the Assembly. It serves as a median value for assessing whether the Assembly is balanced towards longer contigs (higher N50) or shorter contigs (lower N50). N75 is used for the same purpose but is the length is set at 75% of total base content instead of 50%.
- L50 is the number of contigs equal to or longer than the N50 length. In other words, L50, is the minimal number of contigs that contain half the total base content of the Assembly. L75 is used for the same purpose in reference to the N75 length.
-  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
-  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
Module Commit: f6be7c27bbf44a0d65b0250dbdb8079b5df9d7ae