Genome Assembly

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 !!

QuorUM: An Error Corrector for Illumina Reads

Diploid Human Genome Assembly using Pacbio Technology

We are surprised that the researchers are using technology from a company that was supposed to go out of business due to competition from Oxford Nanopore. A new Nature Method paper reports -

Why Are Some Genomes Extremely Large?

In our series on top ten genomes, one candidate represented extremely large genomes. Extremely large genomes are unusual, and it is not unreasonable to ponder how they ended up being so large. A new paper offers insight (h/t:Detlef Weigel @plantevolution).

OPERA-LG: Efficient and Exact Scaffolding of Large, Repeat-rich Eukaryotic Genomes with Performance Guarantees

Performance guarantees? Rarely science papers come with those things :)

Top Ten Genomes - (x) The Human Genome

[Text coming soon, but you know why human genome is among the top ten genomes :) ]

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