待整理

Seed-and-extend aligners

An alignment strategy that first builds a hash table containing the location of each k-mer (seed) within the

reference genome. These algorithms then extend these seeds in both directions to find the best alignment (or 

alignments) for each read. (Martin 2011)

为什么会出现这种情况：

When comparing the lengths and numbers of contigs acquired from de novo assemblies to the predicted number of transcripts from genome projects, the de novo contigs typically are shorter and more numerous.

原因：This is because the assembler cannot join contigs together unless there is enough overlap and coverage in the reads, so that several different contigs will match one mRNA transcript. Biologically, alternative splicing of transcripts also inflates the number of contigs when compared to predictive data from genome projects.

进一步的解决策略：

This is important to keep in mind, especially when analyzing gene expression data based on mapping to a de novo assembly. To minimize this issue, we want to use as many reads as possible in the assembly to maximize the coverage level. The assembler therefore pools the reads from all specified samples, which means that no information about the individual samples can be extracted from the assembly. In order to get that information, we need to map our reads from each sample individually to the assembly once it has been created