FASTQ
Contig 1
Scaffolding
Reference-guided de novo assembly
B
C
A
Read alignment/Mapping
Reference genome/Transcriptome
Reference-based alignment
Unaligned reads
De novo assembly
Contig 2
Contig 3
Fig. 11.3
Basic outline of a reference-based alignment and a de novo
assembly. (A) A reference genome or transcriptome is used for mapping the reads
against this genome. The availability of splicing information for reference transcripts helps in aligning sequencing reads directly in a continuous, memory
efficient manner. (B) Reads are clustered together into contigs by
finding overlaps between the reads. These contigs are then assembled into scaffolds. (C)
Unaligned reads from a reference-based alignment could be assembled using a de novo
strategy that is often referred to as reference-guided de novo
assembly
11 Design and Analysis of RNA Sequencing Data
151
Contig 1
Scaffolding
Reference-guided de novo assembly
B
C
A
Read alignment/Mapping
Reference genome/Transcriptome
Reference-based alignment
Unaligned reads
De novo assembly
Contig 2
Contig 3
Fig. 11.3
Basic outline of a reference-based alignment and a de novo
assembly. (A) A reference genome or transcriptome is used for mapping the reads
against this genome. The availability of splicing information for reference transcripts helps in aligning sequencing reads directly in a continuous, memory
efficient manner. (B) Reads are clustered together into contigs by
finding overlaps between the reads. These contigs are then assembled into scaffolds. (C)
Unaligned reads from a reference-based alignment could be assembled using a de novo
strategy that is often referred to as reference-guided de novo
assembly
11 Design and Analysis of RNA Sequencing Data
151