Editing Shotgun sequencing (section)

== Metagenomic shotgun sequencing ==
Having reads of 400-500 base pairs length is sufficient to determine the species or strain of the organism where the DNA comes from, provided its genome is already known, by using for example a [[k-mer#Genetics and Genomics|''k''-mer based]] [[taxonomy (biology)#Classifying organisms|taxonomic classifier]] software. With millions of reads from next generation sequencing of an environmental sample, it is possible to get a complete overview of any complex microbiome with thousands of species, like the [[gut flora]]. Advantages over 16S rRNA [[amplicon sequencing]] are: not being limited to bacteria; strain-level classification where amplicon sequencing only gets the genus; and the possibility to extract whole genes and specify their function as part of the metagenome.<ref>{{cite journal |last1=Roumpeka |first1=Despoina D. |last2=Wallace |first2=R. John |last3=Escalettes |first3=Frank |last4=Fotheringham |first4=Ian |last5=Watson |first5=Mick |title=A Review of Bioinformatics Tools for Bio-Prospecting from Metagenomic Sequence Data |journal=Frontiers in Genetics |date=6 March 2017 |volume=8 |page=23 |doi=10.3389/fgene.2017.00023 |pmid=28321234 |pmc=5337752 |doi-access=free}}</ref> The sensitivity of metagenomic sequencing makes it an attractive choice for [[clinical metagenomic sequencing|clinical use]].<ref>{{cite journal |last1=Gu |first1=Wei |last2=Miller |first2=Steve |last3=Chiu |first3=Charles Y. |title=Clinical Metagenomic Next-Generation Sequencing for Pathogen Detection |journal=Annual Review of Pathology: Mechanisms of Disease |date=24 January 2019 |volume=14 |issue=1 |pages=319–338 |doi=10.1146/annurev-pathmechdis-012418-012751 |pmid=30355154 |pmc=6345613}}</ref> It however emphasizes the problem of contamination of the sample or the sequencing pipeline.<ref>{{cite journal |last1=Thoendel |first1=Matthew |last2=Jeraldo |first2=Patricio |last3=Greenwood-Quaintance |first3=Kerryl E. |last4=Yao |first4=Janet |last5=Chia |first5=Nicholas |last6=Hanssen |first6=Arlen D. |last7=Abdel |first7=Matthew P. |last8=Patel |first8=Robin |title=Impact of Contaminating DNA in Whole-Genome Amplification Kits Used for Metagenomic Shotgun Sequencing for Infection Diagnosis |journal=Journal of Clinical Microbiology |date=June 2017 |volume=55 |issue=6 |pages=1789–1801 |doi=10.1128/JCM.02402-16 |pmid=28356418 |pmc=5442535
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