We started with 600 million 100mer reads from a genomic library and plotted its K-mer distribution. ...
Maximizing Utility of Available RAMs in K-mer World
Bioinformaticians trying to assemble genomes or transcriptomes from large NGS libraries usually grap...
perl对中文的处理(encode,decode)
Perl从5.6开始已经开始在内部使用utf8编码来表示字符，也就是说对中文以及其他语言字符的处理应该是完全没有问题的。我们只需要利用好Encode这个模块便能充分发挥Perl的utf8字符的优势了。...
How do sequencing errors affect de Bruijn graphs?
Today’s commentary is the fourth in our de Bruijn graph series, but I did not like Roman characters ...
De Bruijn graphs(3)
In earlier commentaries, we introduced the concept of de Bruijn graphs and showed how they were used...
De Bruijn graphs(2)
In the previous post, we discussed how de Bruijn graphs can be constructed for a genome or a large s...
Algorithms for Next-gen Sequence Analysis
The field of next-gen sequence analysis is advancing so rapidly that new algorithms come out almost ...
De Bruijn graphs(1)
New algorithms for short read assembly (categories B and D) often use de Bruijn graphs to store and ...
Format of Velvet Output File ‘Roadmaps’
If you used Velvet genome assembler, you possibly have noticed a file named ‘Roadmaps’ being created...
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...