Editing Sequence assembly (section)

== Types ==
[[File:Types of sequencing assembly.png|thumb|324x324px|Types of sequence assembly]]
There are three approaches to assembling sequencing data:

# De-novo: assembling sequencing reads to create full-length (sometimes novel) sequences, without using a template (see [[de novo sequence assemblers]], [[de novo transcriptome assembly]])<ref name="Baker_2012" />
# Mapping/Aligning: assembling reads by aligning reads against a template (AKA reference). The assembled consensus may not be identical to the template. 
# Reference-guided: grouping of reads by similarity to the most similar region within the reference (step wise mapping). Reads within each group are then shortened down to mimic short reads quality. A typical method to do so is the [[k-mer]] approach. Reference-guided assembly is most useful using [[Third-generation sequencing|long-reads]].<ref name="Wolf" />

Referenced-guided assembly is a combination of the other types. This type is applied on [[Long-read sequencing|long reads]] to mimic [[Massive parallel sequencing|short reads]] advantages (i.e. call quality). The logic behind it is to group the reads by smaller windows within the reference. Reads in each group will then be reduced in size using the k-mere approach to select the highest quality and most probable contiguous (contig). Contigs will then will be joined together to create a scaffold. The final consense is made by closing any gaps in the scaffold.