Tag Archives: assembly

Major new microbial groups expand diversity and alter our understanding of the tree of life

I still believe in revolutions. And sometimes they just happen, almost unnoticed. One such revolution happened on a boring 11th of April 2016 when Laura Hug et al. published their new tree of life in the journal of Nature Microbiology. … Continue reading

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Posted in bioinformatics, community ecology, evolution, genomics, metagenomics, microbiology, next generation sequencing, phylogenetics | Tagged , , , , , , , | Leave a comment

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

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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

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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

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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

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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

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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

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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

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Posted in genomics | Tagged , , | 6 Comments