Question: Error correction of long reads

Question: Error correction of long reads

Hi,

I am going to get some data from plasmid sequencing to identify SNPs on the plasmids. What it is done on the lab is the following:

• The plasmids are purified by size
• We amplify the plasmids using the phi29 polimerase. The polimerase will go trough the plasmid multiple times. Hence we get the same sequence concatenated multiple times. My question is related to this step
• We sequence it using Oxford Nanopore

My question is:

On step two, I wrote that "we get the same sequence concatenated multiple times". For me, this a potential source of information to correct the base calls prior to aligning them to the reference. Since you have the same sequence multiple times ( concatemers). What I would like to know is if there is a tool that uses the information of the concatemers to improve the base calls. I have try to find some methods but found none. I know that PacBio has a similar flavour using the "circular consensus calling", But I have not found any methodological explanation.

thanks!

 

问题:长读的错误修正

你好,

我将从质粒测序中获取一些数据来鉴定质粒上的snp。
在实验室所做的工作如下:

质粒通过大小进行纯化
我们用phi29 polimerase放大质粒。
polimerase会多次穿过质粒。
因此，我们将相同的序列进行多次连接。
我的问题与这一步有关
我们用牛津纳米孔测序
我的问题是:

在第二步中，我写道“我们将相同的序列进行多次连接”。
对我来说，这是一个潜在的信息源，可以在基本调用与引用对齐之前纠正它们。
因为你有相同的序列多次(连体)。
我想知道的是，是否有一个工具使用连接器的信息来改进基础调用。
我试图找到一些方法，但毫无结果。
我知道PacBio也有类似的“循环共识呼唤”的味道，但我还没有找到任何方法上的解释。

谢谢!