Genome Assembly

I Wish Ryan Wick Does not "Publish" his Long Read Assembler Comparison

We encourage our readers to take a look at the comparison of long read assemblers by Ryan Wick and Kathryn Holt. The authors benchmarked five different assemblers, namely Canu, Flye, Ra, Unicycler and Wtdbg2.

Using Synteny in Genome Assembly, an Interesting New Direction?

In this week’s commentary in the membership section, we reviewed the recent advances in the genome assembly field. One paper mentioned there is an excellent PLOS Compbio. review on scaffolding by Jay Ghurye and Mihai Pop. I will skip over the discussion on various long-read technologies and mention a topic with the potential to make substantial improvement in genome assembly.

Scrubbing Tools for Long Noisy Reads from Rayan Chikhi and Collaborators

Pay Attention to These Three New and Impressive Genome Assemblers

The genome assembly field continues to be highly active, and the researchers are still coming up with algorithms making significant speed improvements. The following three projects are definitely worth your attention.

Contamination Nightmare in Microbial Genome Assemblies

While working on RNAse P in microbial genomes, I noticed something very puzzling. An archaeal protein that was never seen before in bacteria was present (and even annotated) in a newly sequenced bacterial genomes. If true, it could completely change the evolutionary understanding of the RNase P protein families.

Practical Dynamic de Bruijn Graphs

The de Bruijn graphs are immensely helpful in assembling Illumina sequences, but they often occupy massive amounts of memory, especially for large raw datasets. Our readers interested in representing de Bruijn graphs in compact space should not miss a recent paper by Victoria Crawford, Alan Kuhnle, Christina Boucher, Rayan Chikhi and Travis Gagie. The paper is published in Bioinformatics, but the journal link is not open-source.

Salmonberry Genomics by High-school Students

Genome assembly algorithms through jigsaw puzzles - III

This is the third installment of “genome assembly algorithms through jigsaw puzzles”. We usually post them here every Tuesday, although we are late this week. You can find all those pieces in one place (and some more) at this link. We are developing this tutorial to explain genome assembly algorithms in a simple manner. In fact, rather than explaining, we expect you to discover the answer by manually solving a jigsaw puzzle. Later we show you how your solutions are related to the commonly used algorithms and their variations.

Genome assembly algorithms through jigsaw puzzles - II

This is the second installment of “genome assembly algorithms through jigsaw puzzles”. We post them here every Tuesday. You can find all those pieces in one place (and some more) at this link. We are developing this tutorial to explain genome assembly algorithms in a simple manner. In fact, rather than explaining, we expect you to discover the answer by manually solving a jigsaw puzzle. Later we show you how your solutions are related to the commonly used algorithms and their variations.

Genome assembly algorithms through jigsaw puzzles

We are developing this tutorial to explain genome assembly algorithms in a simple manner. In fact, rather than explaining, we expect you to discover the answer by manually solving a jigsaw puzzle. Later we show you how your solutions are related to the commonly used algorithms and their variations.

metaSPAdes: a new versatile de novo metagenomics assembler

Mosquito Genome is Shown as the Front Page Image in NY Times

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Assemblytics: a web analytics tool for the detection of assembly-based variants

A New Metagenome Search Program from the LMAT Group

Integration of String and de Bruijn Graphs for Genome Assembly

Safe and Complete Contig Assembly via Omnitigs

HYBRIDSPADES: an algorithm for hybrid assembly of short and long reads

Two Excellent Reviews on Metagenomics

Over the last few days, we have been going through various analysis tools for analysis of metagenomics data sets. The readers working in the same field may find the following two papers useful.

Genome scaffolding with PE-contaminated mate-pair libraries

If Rayan Chikhi is involved, it has to be a good paper.

SPAdes Assembler Team is Looking for Help to Improve Assembler

I got a request from Dmitry Antipov on behalf of SPAdes development team. Please pass it to anyone, who may have the kind of data they are looking for to make this amazing genome assembler even better !!

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