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Tag Archives: assembly
In the pipeline – Part 1: ‘Plan, plan, and plan some more’
So you’ve decided it’s time to finally get around to starting that sequencing project. But before you aimlessly leap into it and generate terabytes of sequencing data, just STOP. It’s far too tempting to rush into sequencing projects for a … Continue reading
Posted in bioinformatics, evolution, genomics, howto, methods, population genetics, Uncategorized
Tagged assembly, bioinformatics, genetics, genomics, In the pipeline, population genetics, Sequencing
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Visualize your genome assemblies
Bandage (a Bioinformatics Application for Navigating De novo Assembly Graphs Easily), is a program that creates visualisations of sequence assemblies that you can interact with. When assembling a genome with your favorite assembler, you are usually building graphs, from which … Continue reading
N50 for transcriptome assemblies
This is the sixth in a series of posts where we explain the N50 (Nx) metric, discuss the problems surrounding it, give solutions to those problems, and suggest an alternative N50 metric for transcriptome assemblies. Transcriptome assemblies are inherently different … Continue reading
Posted in genomics
Tagged assembly, BUSCO, ExN50, rnaQUAST, transcriptome, transrate, Trinity
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A solution to the N50 misassembly problem
This is the fifth in a series of posts where we explain the N50 (Nx) metric, discuss the problems surrounding it, give solutions to those problems, and suggest an alternative N50 metric for transcriptome assemblies. The misassembly problem of N50 that … Continue reading
A solution to the N50 filtering problem
This is the fourth in a series of posts where we explain the N50 (Nx) metric, discuss the problems surrounding it (1, 2), give solutions to those problems, and suggest an alternative N50 metric for transcriptome assemblies. In the two … Continue reading
The N50 misassembly problem
This is the third in a series of posts where we explain the N50 (Nx) metric, discuss the problems surrounding it, give solutions to those problems, and suggest an alternative N50 metric for transcriptome assemblies. In our previous post, we … Continue reading
The N50 filtering problem
This is the second in a series of posts where we explain the N50 (Nx) metric, discuss the problems surrounding it, give solutions to those problems, and suggest an alternative N50 metric for transcriptome assemblies. The problem with N50 (or … Continue reading
What’s N50?
This is the first in a series of posts where we explain the N50 (Nx) metric, discuss the problems surrounding it, give solutions to those problems, and suggest an alternative N50 metric for transcriptome assemblies. Most genome assembly papers include … Continue reading