Editing Sequence analysis (section)

=== Quality control and preprocessing === 
Quality control assesses the quality of sequencing reads obtained from the sequencing technology (e.g. [[Illumina, Inc.|Illumina]]). It is the first step in sequence analysis to limit wrong conclusions due to poor quality data. The tools used at this stage depend on the sequencing platform. For instance,  FastQC checks the quality of short reads (including RNA sequences), Nanoplot or PycoQC are used for [[third-generation sequencing | long read sequences]] (e.g. Nanopore sequence reads), and MultiQC aggregates the result of FastQC in a webpage format.<ref>{{cite web |last1=Batut |first1=Bérénice |last2=Doyle |first2=Maria |last3=Cormier |first3=Alexandre |last4=Bretaudeau |first4=Anthony |last5=Leroi |first5=Laura |last6=Corre |first6=Erwan |last7=Robin |first7=Stéphanie |last8=nil |first8=gallantries |last9=Hyde |first9=Cameron |title=Quality Control (Galaxy Training Materials) |url=https://training.galaxyproject.org/training-material/topics/sequence-analysis/tutorials/quality-control/tutorial.html |website=Galaxy Training! |date=3 November 2023 |access-date=26 April 2024}}</ref><ref name=galaxy1>{{cite journal |last1=Hiltemann |first1=Saskia |last2=Rasche |first2=Helena |last3=Gladman |first3=Simon | display-authors = 2 |title=Galaxy Training: A Powerful Framework for Teaching! |journal=PLOS Computational Biology |date=January 2023 |volume=19 |issue=1 |pages=e1010752 |doi=10.1371/journal.pcbi.1010752 |doi-access=free |pmid=36622853 |pmc=9829167 |bibcode=2023PLSCB..19E0752H }}</ref><ref name=galaxy2>{{cite journal |last1=Batut |first1=Bérénice |last2=Hiltemann |first2=Saskia | display-authors = 1 |title=Community-Driven Data Analysis Training for Biology |journal=Cell Systems |date=2018 |volume=6 |issue=6 |pages=752–758.e1 |doi=10.1016/j.cels.2018.05.012 |pmid=29953864 |pmc=6296361 |url=https://doi.org/10.1016%2Fj.cels.2018.05.012}}</ref> 

Quality control provides information such as read lengths, [[GC-content|GC content]], presence of adapter sequences (for short reads), and a quality score, which is often expressed on a [[phred quality score|PHRED scale]].<ref name=sequence_analysis>{{cite journal |last1=Prijibelski |first1=Andrey B. |last2=Korobeynikov |first2=Anton I. |last3=Lapidus |first3=Alla L. |title=Sequence Analysis |journal=Encyclopedia of Bioinformatics and Computational Biology |date=September 2018 |volume=3 |pages=292–322 |doi=10.1016/B978-0-12-809633-8.20106-4 |isbn=978-0-12-811432-2 |url=https://doi.org/10.1016/B978-0-12-809633-8.20106-4|url-access=subscription }}</ref> If adapters or other artifacts from PCR amplification are present in the reads (particularly short reads), they are removed using software such as Trimmomatic<ref>{{cite journal |last1=Bolger |first1=Anthony M. |last2=Lohse |first2=Marc |last3=Usadel |first3=Bjoern |title=Trimmomatic: a flexible trimmer for Illumina sequence data |journal=Bioinformatics |date=April 2014 |volume=30 |issue=15 |pages=2114–2120 |doi=10.1093/bioinformatics/btu170 |pmid=24695404 |pmc=4103590 |url=https://doi.org/10.1093/bioinformatics/btu170}}</ref> or Cutadapt.<ref>{{cite journal |last1=Marcel |first1=Martin |title=Cutadapt removes adapter sequences from high-throughput sequencing reads |journal=EMBnet.journal |date=2011 |volume=17 |page=10 |doi=10.14806/ej.17.1.200 |url=https://doi.org/10.14806/ej.17.1.200}}</ref>