Editing Sequence assembly (section)

== Quality control ==
Most sequence assemblers have some algorithms built in for quality control, such as [[Phred (software)|Phred]].<ref>{{cite journal | vauthors = Cock PJ, Fields CJ, Goto N, Heuer ML, Rice PM | title = The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants | journal = Nucleic Acids Research | volume = 38 | issue = 6 | pages = 1767–1771 | date = April 2010 | pmid = 20015970 | pmc = 2847217 | doi = 10.1093/nar/gkp1137 }}</ref> However, such measures do not assess assembly completeness in terms of gene content. Some tools evaluate the quality of an assembly after the fact.

For instance, BUSCO (Benchmarking Universal Single-Copy Orthologs) is a measure of gene completeness in a genome, gene set, or [[transcriptome]], using the fact that many genes are present only as single-copy genes in most genomes.<ref name="Simão_2015">{{cite journal | vauthors = Simão FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM | title = BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs | journal = Bioinformatics | volume = 31 | issue = 19 | pages = 3210–3212 | date = October 2015 | pmid = 26059717 | doi = 10.1093/bioinformatics/btv351 }}</ref> The initial BUSCO sets represented 3023 genes for [[vertebrate]]s, 2675 for [[arthropod]]s, 843 for [[Animal|metazoans]], 1438 for [[Fungus|fungi]] and 429 for [[eukaryote]]s. This table shows an example for human and fruit fly genomes:<ref name="Simão_2015" />
{| class="wikitable"
|+BUSCO notation assessment results (Complete, Duplicate, Fragmented, Missing in %)
!Species
!genes
!Complete
!Duplicated
!Fragmented
!Missing
!n (BUSCO gene number)
|-
|''[[Human|Homo sapiens]]''
|20,364 
|99
|1.7
|0.0
|0.0
|3,023
|-
|''[[Drosophila melanogaster]]''
|13,918
|99
|3.7
|0.2
|0.0
|2,675
|}