1. 测序前的准备 搜集物种相关信息，比如基因组大小，杂合度， 1.1 获取基因组大小 基因组大小的获取关系到对以后组装结果的大小的正确与否判断；基因组太大（>10Gb），超出了目前denovo...
Bioinformatics
Bioinformatics
Genomics
基因组组装软件velvet以及参数优化
利用k-mer组装的基因组的软件现在已经很多了，例如soapdenovo，velvet等等。PLoB上已经有不少关于velvet的软件的介绍，今天再次谈谈velvet这个软件，主要是推荐一些velve...
Genomics
K-mer应用实例分析
We started with 600 million 100mer reads from a genomic library and plotted its K-mer distribution. ...
Genomics
Maximizing Utility of Available RAMs in K-mer World
Bioinformaticians trying to assemble genomes or transcriptomes from large NGS libraries usually grap...
Genomics
De Bruijn graphs(2)
In the previous post, we discussed how de Bruijn graphs can be constructed for a genome or a large s...
Bioinformatics
De Bruijn graphs(1)
New algorithms for short read assembly (categories B and D) often use de Bruijn graphs to store and ...
Genomics
Format of Velvet Output File ‘Roadmaps’
If you used Velvet genome assembler, you possibly have noticed a file named ‘Roadmaps’ being created...
Bioinformatics
Efficient Methods for Counting K-mers
当拿到转录组数据或者基因组数据后，在做拼接以及其他一系列的分析之前，我们一般会做一个K-mer频率分布分析，下面是目前常用的几种计算K-mer的算法和软件。 A. Bloom Filter-based...