Article Archive

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Hybrid Metagenomic Assembler OPERA-MS

Genome Assembly is a Nearly Solved Problem with Long Reads

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

Using Synteny in Genome Assembly, an Interesting New Direction?

Scrubbing Tools for Long Noisy Reads from Rayan Chikhi and Collaborators

Pay Attention to These Three New and Impressive Genome Assemblers

Contamination Nightmare in Microbial Genome Assemblies

Practical Dynamic de Bruijn Graphs

Salmonberry Genomics by High-school Students

Genome assembly algorithms through jigsaw puzzles - III

Genome assembly algorithms through jigsaw puzzles - II

Genome assembly algorithms through jigsaw puzzles

metaSPAdes: a new versatile de novo metagenomics assembler

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

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

Genome scaffolding with PE-contaminated mate-pair libraries

SPAdes Assembler Team is Looking for Help to Improve Assembler

QuorUM: An Error Corrector for Illumina Reads

Diploid Human Genome Assembly using Pacbio Technology

Why Are Some Genomes Extremely Large?

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

Top Ten Genomes - (x) The Human Genome

Top Ten Genomes - (viii) Trichomonas vaginalis

Top Ten Genomes - (vii) Bladderwort

Top Ten Genomes - (ix) Pacific oyster

Top Ten Genomes – (vi) Oxytricha trifallax for MIC and MAC in Ciliates

Top Ten Genomes - (v) Ich

Top Ten Genomes - (iv) Methanococcus jannaschii

Top Ten Genomes - (iii) Paris japonica

Top Ten Genomes – (ii) Dynamically Changing Genomes

Top Ten Genomes - (i) Lamprey

On the readability of overlap digraphs

Metassembler: Merging and optimizing de novo genome assemblies

FermiKit: assembly-based variant calling for Illumina resequencing data

ScaffMatch: Scaffolding Algorithm Based on Maximum Weight Matching

Using de Bruijn Graphs for Short-read Assembly - (ii)

Using de Bruijn Graphs for Short-read Assembly - (i)

LINKS - Long Interval Nucleotide K-mer Scaffolder

After SPAdes and Rosalind, Russians Fail Again

MEDUSA: a Multi-draft Based Scaffolder

The Current Status of the Introductory Book on Genome Assembly

Perfect Genome Assembly - BGI's Solution

Chromosome-scale Shotgun Assembly using an in vitro Method for Long-range Linkage

Minia 2.0.1 is Released

An Update on the Introductory Book on Genome Assembly

Parallel de Bruijn Graph Construction and Traversal for de novo Genome Assembly

Do Read Errors Matter for Genome Assembly?

Compression of High Throughput Sequencing Data with Probabilistic de Bruijn

Dear BGI, Please Stop 'Revealing' Any More 'Insights' :)

Misassembly Detection using Paired-End Sequence Reads and Optical Mapping Data

An Easy-to-follow Introductory Book on NGS Assembly Algorithms

Variable-Order de Bruijn Graphs

MEGAHIT - An Ultra-fast Single-node Solution for Large and Complex Metagenomics Assembly via Succinct de Bruijn Graph

Genome Informatics 2014 Conference (#gi2014)

T. Ryan Gregory Starts 'Evolution Consulting Service' after Reading Gibbon Paper in Nature

Tutorial on David Tse's Work on DNA/RNA Assembly Presented at ISIT 2014

Genome Assembly - Discussion on Standardization of How to Represent Assembled

Minia's New Home - GATB (Genome Assembly & Analysis Tool Box)

The New K-mer Counter and a Genome Assembly - (ii)

The New K-mer Counter and a Genome Assembly - (i)

Bayesian Genome Assembly and Assessment by Markov Chain Monte Carlo Sampling

Our Bootstrapped Genome Paper Is Published

SPAdes Group's Long-awaited Repeat Resolver Paper is Published

Minimizer Success - Disk-based Genome Sequencing Data Compression

Lighter: fast and memory-efficient error correction without counting

Sponge Jelly Genome is Studied to Find Evolutionary Origins of Neural Systems

What is the State of the Art for Bacterial Genome Assembly from Illumina Reads?

Posters and Slides from #BoG14

At #BoG14, Posters Are Far More Interesting than Talks

Efficient de novo Assembly of Highly Heterozygous Genomes from Whole-genome Shotgun Short Reads

I Often Repeat Repeat Myself, I Often Repeat Repeat

SplitMEM: Graphical Pan-genome Analysis with Suffix Skips

On Algorithmic Complexity of Biomolecular Sequence Assembly Problem

Peanut Genome Released

BESST Scaffolder

A Plant Genome Assembly Question

Going Through the Code of SOAPdenovo-trans

JGI Looking Beyond Sequencing to Become 'Cutting Edge' Press Release Generating

Why is Gene Myers Dancing? Answer - Long Reads !!

A Question on MaSuRCA Assembler

Keith Robison's Perfect Scaffolder Delivered, What Next?

dipSpades Beats Haplomerger Hands Down in Diploid Assembly

An Opinionated History of Genome Assembly Algorithms - (ii)

An Opinionated History of Genome Assembly Algorithms - (i)

What is the Cost of Scaling Up Genome Assembly Massively?

De Novo Assembly of Human Genome with Only 1.5 GB RAM

Unicorn Genome Published

SPAdes 3.0 Released with PacBio Hybrid Assembly Module

BGI Applies for Genome Assembly Patent, Claims Priority/Benefits from Chinese

#UCDAssemble Workshop - Friday Update

#UCDAssemble Workshop Covering Genome Assembly

Burrows-Wheeler Transform (BWT) is de Bruijn Graph is BWT

Genome Assembly - An Exchange between Two Experts

PLOS One Paper - "Comparing Memory-Efficient Genome Assemblers on Stand-Alone and Cloud Infrastructures"

Genome Informatics Meeting at CSHL #GI2013

SPAdes Assembler, Python in Bio, US Effect, Return of Lysenko and Other Stories

SOAPdenovo2 on Github, Now 'Searching Soul' on Assemblers

New Paper on Comparing Genome Assemblies

Modularizing SOAPdenovo2 Code into Four Components

Chinese Hamster Genome Sequenced from Sorted Chromosomes

Jumping Read Assembler - Before it is News

BGI's K-mer Analysis Paper

"Hydrogen Atom" to Learn Inner Workings of Genome Assembly Programs

Cerulean: A Hybrid Assembly using High Throughput Short and Long Reads

SOAPdenovo2 Demystified, BWA Mystified

Detecting Superbubbles in Assembly Graphs

Reducing Assembly Complexity of Microbial Genomes with Single-molecule Sequencing

Two Important Papers Published - Assemblathon and First Genome using Moleculo

From de Bruijn Graph to Minimal Promoter

Assemblathon, GAGE and Four Dimension of Evaluating Genome Assembly Programs

Metagenomics of Buried Lake in Antarctica - Paper Differs from Earlier Press

Cleverness of the Ray Assembler

More on Succint de Bruijn Graph

Genome Sequence of an Ancient Horse

Very Helpful Preprocessing Module for Those Interested in Assembling Genomes

MS-thesis: FPGA-based Genome Assembler

Philip Ashton, Assembly Optimisation - Impact of Error Correction and a New Assembler, SPAdes

Let's Lend Ruibang a Helping Hand to Fix SOAPdenovo2

Jared Simpson's 2011 Talk at JGI on Memory Efficient Assembly

De novo Assembly is not at all Black Art

#Bog13: Simultaneous Assembly of Thousands of Human Genomes - Erik Garrison from Marthlab

GAM-NGS and REAPR Papers are Published

SPAdes and MaSuRCA Assemblers Performed Best in GAGE-B Evaluation

How about a Chaotic Genome Assembler?

Should Genome Assembly Improve with More and More Reads?

#bog13 Posters on Pine and Coelacanth

NGS Assembly Programs - What Hash Functions Do They Use?

Biology of Genomes Conference 2013

Good Riddance - "Death of the Genome Paper"

Philip Ashton: Assessment of Assembly

Turtle - the Luckiest Animal of the Month

Surprise of the Day - Zebrafish Genome 'Published'

Informed and Automated k-Mer Size Selection for Genome Assembly

Genome of Western Painted Turtle

Genome of a 'Living Fossil'

Optimal DNA Shotgun Sequencing: Noisy Reads are as Good as Noiseless Reads

Genome Size Estimation and Polymorphism from K-mer Distribution

Final Words on De Novo Assembly of Complex Genomes

Step by Step Guide on Genome Assembly with blasr and python

Genome Assembly from Random Sequence

Overlap-Layout-Consensus versus de Bruijn Graph Assemblers

Bootstrapped Genome Project (iv) - More on Triplicate Experiments

De Bruijn Graph Tutorials are Here

Bootstrapped Genome Project (iii) – on Mindless Triplicate Experiments

Lamprey Genome Paper is not Lucky Either

Lamprey Genome Shows When Humans Evolved Jaws, Matching Arms, Legs and More

Titus Brown's Thoughts on the Assemblathon 2 paper

Slides from AGBT Conference

Genome Reassembly with High-throughput Sequencing Data

Possibly the Best Book on Personal Genomics and Personalized Medicine

SCARPA: Scaffolding Algorithm from Hapsembler Group

Hapsembler - An Assembler for Highly Polymorphic Genomes

Gut Metagenome in Children during Cholera and Recovery

DSK: K-mer Counting with Very Low Memory Usage

SOAPdenovo2 Demystified - A Rough Guideline of Functionality

More SOAPdenovo2 Commentaries Will Come in February

SOAPdenovo2 Demystified – part (b) [multi-thread implementations]

Assembling Large, Complex Environmental Metagenomes

Notes on Assemblathon Paper

CEGMA - a pipeline to accurately annotate core genes in eukaryotic genomes

Assemblathon 2 Paper is Available at Arxiv !!

Expect Some Really Amazing Metagenome Data from Russia

Working Through the Code of Cortex Variant Assembler

High-throughput Microbial Population Genomics using the Cortex Variation Assembler

Three Helpful Guides for Those Working on Genome Assembly

A Quantitative Comparison of DNA Sequence Assembly Programs

SOAPdenovo2 Demystified - part (a)

SOAPdenovo2 Demystified - part 1

Optimal Assembly for High Throughput Shotgun Sequencing

Genomes Published in 2012

January is Our 'Learn How SOAPdenovo2 Works' Month

Our First Look at SOAPdenovo2 Source Code

Should SOAPdenovo2 Source Code be Made Public?

Ray Meta: Scalable de Novo Metagenome Assembly and Profiling

More Details on Velvet Roadmaps File Based on Reader's Question

Recipes for Assembling Genomes from GAGE

Exploring Single-sample SNP and indel Calling with Whole-Genome Assembly

Challenges in Assembling Fish Genomes

Ray Cloud Browser for Viewing de Bruijn Graphs

Various Developments - 11/26/2012

Ph. D. Thesis: Computational Metagenomics: Network, Classification and Assembly

Next Generation Shotgun Sequencing and the Challenges of de novo Genome Assembly

Rectangular Graph Algorithm

Taking the 'Eulearian Path'

The Chinese Mailman, Who Does not Like to Walk

IPython Notebook and de Bruijn Graph

Going Through the SPAdes Code (Rectangular Graph)

SiBELia/SyntenyFinder - A de Bruijn Graph-based Tool for Finding Syntenies

SEQuel - A Software Tool for Improving Assembled Genome

de Bruijn Graphs Simplified

De Bruijn Graph of a Palindromic Sequence

From Multiple Kmers to Multi-kmer de Bruijn Graph

Are Ultra-low RAM Assemblers Useful for those with Kick-ass Servers?

Succinct de Bruijn Graphs from Tetsuo Shibuya's Group

What are the Puzzle Pieces in a Rectangle Graph?

De novo Genome Assembly: What Every Biologist Should Know

Perfect Hash Algorithm of Meraculous Assembler

Minia Assembler and French Revolution

Heads Up for Readers - SPAdes vs Ray Benchmarking is Done

COPE (for Joining PE Reads) and Arapan-S (for Small Genomes)

A Comment from Developer of Ray Assembler

Pacific Oyster Genome Published

Starting to Understand the SPAdes Papers

Creating Confusion

SOAPdenovo2 Binary is on SourceForge

From de Bruijn Graphs to Rectangle Graphs for Genome Assembly

Telescoper: de novo Assembly of Highly Repetitive Regions

How Do Haplotype Differences Appear to de Bruijn Assemblers ?

HapCompass: An Elegant Use of Graphs for Haplotype Assembly/Phasing

Parallel de novo Assembly of Large Genomes from High-Throughput Short Reads

Genome Assembly - MERmaid and Meraculous

Thesis Slides from Rayan Chikhi

Building an NGS Reference List (SNP/variant calling category)

Building an NGS Reference List (de novo assembly category)

Mixing Illumina and PacBio Data for Genome Finishing

Using SOAPdenovo2 with SOLiD Sequences

An Efficient Preprocessing Module for Joining Paired end Reads before Assembly

Quip, Minia, SlimGene and Titus Brown's paper on Scaling Metagenome

HaploMerger: A Software Tool for Assembling Highly Polymorphic Genomes

Testing SOAPdenovo2 Prerelease – V (map and scaff)

Testing SOAPdenovo2 Prerelease - IV (building contigs)

Testing SOAPdenovo2 Prelease Version - III

Testing SOAPdenovo2 Pre-release Version - II (pregraph_sparse)

Testing SOAPdenovo2 Pre-release Version

What is Wrong with N50? How can we make it better?

What is Wrong with N50? How can we make it better? - part II

SOAPdenovo2 and Other News from BGI

An Intuitive Explanation for Running Velvet with Varying K-mer Sizes

Excellent Introductory Tutorials for Velvet, ABySS, Bowtie, BWA and Newbler

An Explanation of Velvet Parameter exp_cov

Can Trinity be Used for Genome Assembly?

Untangling Genomes from Metagenomes (Attn. SOLiD users)

String Graph of a Genome

String Graph Assembler

Velvet Optimizer and MetaVelvet

Format of Velvet Output File 'Roadmaps'

If You are New Here

Sharing a K-mer Story

Two Simple Rules

Partitioning Libraries to Fit Small RAM Size

Updating a de Bruijn Assembler Code for Color Space Data in Six Easy Steps

K-mer Sizes for Genome Assembly

Watching a de Bruijn Assembler in Action (Contrail)

Maximizing Utility of Available RAMs in K-mer World

Do de Bruijn Assemblers Work in Color Space?

Contrail - A de Bruijn Genome Assembler that uses Hadoop

Using Mate Pair Information in de Bruijn Graphs

A Drawback of de Bruijn Graph Approach

How do sequencing errors affect de Bruijn graphs?

De Bruijn Graphs - III

De Bruijn graphs - II

De Bruijn graphs - I