Editing Sequence analysis (section)

=== Read alignment ===

At this step, sequencing reads whose quality have been improved are mapped to a [[reference genome]] using alignment tools like BWA<ref>{{cite journal |last1=Li |first1=Heng |last2=Durbin |first2=Richard |title=Fast and accurate short read alignment with Burrows–Wheeler transform |journal=Bioinformatics |date=July 2009 |volume=25 |issue=14 |pages=1754–1760 |doi=10.1093/bioinformatics/btp324 |pmid=19451168 |url=https://doi.org/10.1093/bioinformatics/btp324}}</ref> for short DNA sequence reads, minimap<ref>{{cite journal |last1=Li |first1=Heng |title=Minimap and miniasm: fast mapping and de novo assembly for noisy long sequences |journal=Bioinformatics |date=March 2016 |volume=32 |issue=14 |pages=2103–2110 |doi=10.1093/bioinformatics/btw152 |pmid=27153593 |pmc=4937194 |url=https://doi.org/10.1093/bioinformatics/btw152}}</ref> for long read DNA sequences, and STAR<ref>{{cite journal |last1=Dobin |first1=Alexander |last2=Davis |first2=Carrie A. |last3=Schlesinger |first3=Felix | display-authors = 2 |title=STAR: ultrafast universal RNA-seq aligner |journal=Bioinformatics |date=October 2012 |volume=29 |issue=1 |pages=15–21 |doi=10.1093/bioinformatics/bts635 |pmid=23104886 |url=https://doi.org/10.1093/bioinformatics/bts635|pmc=3530905 }}</ref> for RNA sequence reads. The purpose of mapping is to find the origin of any given read based on the reference sequence. It is also important for detecting variations or [[molecular phylogenetics|phylogenetic studies]].
The output from this step, that is, the aligned reads, are stored in compatible file formats known as SAM, which contains information about the reference genome as well as individual reads. Alternatively, [[Binary Alignment Map|BAM file]] formats are preferred as they use much less desk or storage space.<ref name=sequence_analysis/>

'''Note''': This is different from sequence alignment which compares two or more whole sequences (or sequence regions) to quantify similarity or differences or to identify an unknown sequence (as discussed below).

'''The following analyses steps are peculiar to DNA sequences:'''