Editing DNA sequencing (section)

== Computational challenges ==
The sequencing technologies described here produce raw data that needs to be assembled into longer sequences such as complete genomes ([[sequence assembly]]). There are many computational challenges to achieve this, such as the evaluation of the raw sequence data which is done by programs and algorithms such as [[Phred (software)|Phred]] and [[Phrap]]. Other challenges have to deal with [[Repetitive DNA|repetitive]] sequences that often prevent complete genome assemblies because they occur in many places of the genome. As a consequence, many sequences may not be assigned to particular [[chromosome]]s. The production of raw sequence data is only the beginning of its detailed [[Bioinformatics|bioinformatical]] analysis.<ref name="pmid24727769">{{cite journal | vauthors = Severin J, Lizio M, Harshbarger J, Kawaji H, Daub CO, Hayashizaki Y, Bertin N, Forrest AR | title = Interactive visualization and analysis of large-scale sequencing datasets using ZENBU | journal = Nat. Biotechnol. | volume = 32 | issue = 3 | pages = 217–19 | year = 2014 | pmid = 24727769 | doi = 10.1038/nbt.2840 | s2cid = 26575621 }}</ref> Yet new methods for sequencing and correcting sequencing errors were developed.<ref>{{cite journal | vauthors = Shmilovici A, Ben-Gal I | title = Using a VOM model for reconstructing potential coding regions in EST sequences | journal = Computational Statistics | year = 2007 | volume = 22 | issue = 1 | pages = 49–69 | doi = 10.1007/s00180-007-0021-8 | s2cid = 2737235 | url = http://www.eng.tau.ac.il/~bengal/VOM_EST.pdf | access-date = 10 January 2014 | archive-date = 31 May 2020 | archive-url = https://web.archive.org/web/20200531014400/http://www.eng.tau.ac.il/~bengal/VOM_EST.pdf | url-status = dead }}</ref>

=== Read trimming ===
Sometimes, the raw reads produced by the sequencer are correct and precise only in a fraction of their length. Using the entire read may introduce artifacts in the downstream analyses like genome assembly, SNP calling, or gene expression estimation. Two classes of trimming programs have been introduced, based on the window-based or the running-sum classes of algorithms.<ref>{{cite journal | vauthors = Del Fabbro C, Scalabrin S, Morgante M, Giorgi FM | title = An Extensive Evaluation of Read Trimming Effects on Illumina NGS Data Analysis | journal = PLOS ONE | volume = 8 | issue = 12 | pages = e85024 | year = 2013 | pmid = 24376861 | pmc = 3871669 | doi = 10.1371/journal.pone.0085024 | bibcode = 2013PLoSO...885024D | doi-access = free }}</ref> This is a partial list of the trimming algorithms currently available, specifying the algorithm class they belong to:

{| class="wikitable"
|+ Read Trimming Algorithms
! Name of algorithm !! Type of algorithm
|-
| Cutadapt<ref name=cutadapt>{{cite journal|last1=Martin|first1=Marcel|title=Cutadapt removes adapter sequences from high-throughput sequencing reads|journal=EMBnet.journal|date=2 May 2011|volume=17|issue=1|page=10|doi=10.14806/ej.17.1.200|doi-access=free}}</ref> || Running sum
|-
| ConDeTri<ref name=condetri>{{cite journal | vauthors = Smeds L, Künstner A | title = ConDeTri--a content dependent read trimmer for Illumina data | journal = PLOS ONE | volume = 6 | issue = 10 | pages = e26314 | date = 19 October 2011 | pmid = 22039460 | pmc = 3198461 | doi = 10.1371/journal.pone.0026314 | bibcode = 2011PLoSO...626314S | doi-access = free }}</ref> || Window based
|-
| ERNE-FILTER<ref name="erne-bs5">{{cite book| vauthors = Prezza N, Del Fabbro C, Vezzi F, De Paoli E, Policriti A |title=Proceedings of the ACM Conference on Bioinformatics, Computational Biology and Biomedicine |chapter=Erne-Bs5 |date=2012|volume=12|pages=12–19|doi=10.1145/2382936.2382938|isbn=9781450316705|s2cid=5673753}}</ref> || Running sum
|-
| FASTX quality trimmer || Window based
|-
| PRINSEQ<ref name=prinseq>{{cite journal | vauthors = Schmieder R, Edwards R | title = Quality control and preprocessing of metagenomic datasets | journal = Bioinformatics | volume = 27 | issue = 6 | pages = 863–4 | date = March 2011 | pmid = 21278185 | pmc = 3051327 | doi = 10.1093/bioinformatics/btr026 }}</ref> || Window based
|-
| Trimmomatic<ref name=trimmomatic>{{cite journal | vauthors = Bolger AM, Lohse M, Usadel B | title = Trimmomatic: a flexible trimmer for Illumina sequence data | journal = Bioinformatics | volume = 30 | issue = 15 | pages = 2114–20 | date = August 2014 | pmid = 24695404 | pmc = 4103590 | doi = 10.1093/bioinformatics/btu170 }}</ref> || Window based
|-
| SolexaQA<ref name=solexaqa>{{cite journal | vauthors = Cox MP, Peterson DA, Biggs PJ | title = SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data | journal = BMC Bioinformatics | volume = 11 | issue = 1 | pages = 485 | date = September 2010 | pmid = 20875133 | pmc = 2956736 | doi = 10.1186/1471-2105-11-485 | doi-access = free }}</ref> || Window based
|-
| SolexaQA-BWA || Running sum
|-
| Sickle || Window based
|}