一般在基因组组装中，我们常用的拼接方法是，对测序得到的二代数据直接用soapdenovo等软件进行基因组组装。但是这些方法一般只是适用于单一的基因组序列。 最近做的一个课题是从植物混合测序的数据中（核...
Genomics
Genomics
Genomics
Running newbler: more de novo assembly parameters
There is a long list of options/flags/parameters for a newbler assembly, some of which have been tre...
Bioinformatics
Running newbler: de novo assembly
This post is about how to start up newbler for de novo assembly projects. I will describe setting up...
Genomics
Newbler output VI: the ‘status’ files
The files that are the topic of this post are all tables, i.e. tab separated text files. The ‘status...
Genomics
Newbler output V: the 454ContigScaffolds.txt and 454ScaffoldContigs.fna
In the post on what is new in newbler version 2.6, I introduced the -scaffold option. Briefly, with ...
Genomics
Newbler output IV: on ultra-short and single-read contigs
Sometimes you might observe very short contigs, some even having high read depth. You might see thes...
Genomics
Newbler output II: contigs and scaffolds sequence files, and the 454Scaffolds.txt file
The files most people are after when they do an assembly must be these: the actual contig and scaffo...
Bioinformatics
Newbler output I: the 454NewblerMetrics.txt file
With this post, I’ll start going through the output files newbler generates. Some of these will be d...
Genomics
newbler输出结果文件454ContigGraph.txt内容介绍
The single file I’ll discuss today has in fact almost the entire assembly in it, besides the actual ...
Genomics
How newbler works
I thought to start by explaining briefly how newbler works. I’ll do this by following the output new...