Homolog.us Welcomes #PAGXXI Attendees With a Blog Guide

Homolog.us Welcomes #PAGXXI Attendees With a Blog Guide


We have been to Plant and Animal Genome (PAG) conference in San Diego several times. In addition to being a fantastic conference, it also lets everyone see sun during cloudy winter days in most of North America, Europe and northern Asia. We are unable to visit to visit this year, but are keeping track of events through the high-tech 24 hour news feed (aka Twitter).

To celebrate the opening of the conference, we created a large guide of all our blog posts over the last two years.

Our Objectives

A Road Map for our Journey through the Transcriptomic Maze

Introductory Articles on Bioinformatics

A beginner’s guide to bioinformatics - part I

A beginner’s guide to bioinformatics - part II

Algorithms for Next-gen Sequence Analysis

Large Computer, Distributed Cluster or Amazon Cloud?

Must-have Tools for a Bioinformatician

Three Helpful Guides for Those Working on Genome Assembly

On de Bruijn Graphs

De Bruijn graphs - I

De Bruijn graphs - II

De Bruijn Graphs - III

How do sequencing errors affect de Bruijn graphs?

De Bruijn Graphs for Alternative Splicing and Repetitive Regions

A Drawback of de Bruijn Graph Approach

De Bruijn Graphs for Alternative Splicing and Repetitive Regions

Using Mate Pair Information in de Bruijn Graphs

Contrail - A de Bruijn Genome Assembler that uses Hadoop

Watching a de Brujin Graph Assembler in Action (Contrail)

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

Ray Cloud Browser for Viewing de Bruijn Graphs

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

Creating Confusion

Efficient Methods for Counting K-mers

Optimizing Sequence Assemblies

Maximizing Utility of Available RAMs in K-mer World

K-mer Sizes for Genome Assembly

Partitioning Libraries to Fit Small RAM Size

K-mer distribution of a transcriptome

Sharing a K-mer Story

De Bruijn Graph of a Palindromic Sequence

de Bruijn Graphs Simplified

From de Bruijn Graphs to Rectangle Graphs for Genome Assembly

From Multiple Kmers to Multi-kmer de Bruijn Graph

Gossamer Succinct data structure for efficient storage of de Bruijn graphs

How Do Haplotype Differences Appear to de Bruijn Assemblers ?

IPython Notebook and de Bruijn Graph

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

Succinct de Bruijn Graphs from Tetsuo Shibuyas Group

Challenges in Assembling Fish Genomes

De novo Genome Assembly: What Every Biologist Should Know

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

Excellent Slides from Fisherman Lex on Combining PacBio and Short Reads

Genome Assembly MERmaid and Meraculous

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

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

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

Optimal Assembly for High Throughput Shotgun Sequencing

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

Telescoper: de novo Assembly of Highly Repetitive Regions

Recipes for Assembling Genomes from GAGE

Pacific Oyster Genome Published

SEQuel A Software Tool for Improving Assembled Genome

Three Helpful Guides for Those Working on Genome Assembly

Thesis Slides from Rayan Chikhi

Metagenome Assembly

Velvet Optimizer and MetaVelvet

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

Ray Meta: Scalable de Novo Metagenome Assembly and Profiling

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

Ultrafast Clustering Algorithms for Metagenomic Sequence Analysis

Untangling Genomes from Metagenomes (Attn. SOLiD users)

Transcriptome Assemblers

De Novo Transcriptome Assemblers - Oases, Trinity, etc.

De Novo Transcriptome Assemblers Oases, Trinity, etc. - II

De Novo Transcriptome Assemblers Oases, Trinity, etc. III

De Novo Transcriptome Assemblers Oases, Trinity, etc. IV

Explaining Output of Trinity Component - Inchworm

Output of Oases Transcriptome Assembler

[Custom Array Experiment Complete Pipeline

R for Transcriptomics

A Question on de Bruijn Graphs of Transcriptomes (RNA-seq)

A Strategy for Running Trinity on Very Large NGS Library or Reducing Number of Genes

Algorithmic Differences between Oases and Trinity

An Experience with New Trinity

Can Trinity be Used for Genome Assembly?

Digital and Analog Transcriptomics

Do We Need to Reinterpret all Published Gene Expression Studies?

Few Simple Trinity Tips

Many RNA-seq Presentations/Posters at ASHG Conference, San Francisco

Oases Transcriptome Assembler

Trinity Run Completed. Is This Typical?

Two RNAseq Papers Worm and Sea urchin

Standard Steps for RNAseq Experiment

Using R for Transcriptome Analysis - I

Comparison of data analysis packages

R / Bioconductor (limma)

Hadoop

Using Hadoop for Transcriptomics - An Example to Get Started

Hadoop Example - FAQ

Contrail - A de Bruijn Genome Assembler that uses Hadoop

Watching a de Brujin Graph Assembler in Action (Contrail)

Hadoop at JGI (NERSC)?

Sequence Alignment Methods

Finding us in homolog.us

Finding us in homolog.us - part II

Finding us in homolog.us III (Search Algorithm and Indexing)

Burrows Wheeler transform - Suffix Arrays and FM Index

Data Compression Algorithms

Suffix Arrays

Burrow Wheeler Transform Matlab Code, Animation

Bowtie Alignment with and without Quality Score

Burrows Wheeler Transform in Animation

STAR: Really Kick-ass RNA-seq Aligner

The World of Mapping Programs

SOLiD/Color Space

The Mathematics of Color Space Sequencing

Do de Bruijn Assemblers Work in Color Space?

Trinity and Contrail for Color Space

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

NCBI GEO Database

A Bird’s Eye View of NCBI GEO Database

A Bird’s Eye View of NCBI GEO Database - II

Transcriptomic Research around the Globe

Where are the global hotbeds of transcriptomic research?

GEO and SRA - Quarterly Growth in Transcriptomic Research

Velvet

Format of Velvet Output File Roadmaps

More Details on Velvet Roadmaps File Based on Readers Question

An Explanation of Velvet Parameter exp_cov

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

More Details on Velvet Roadmaps File Based on Readers Question

SPAdes

Going Through the SPAdes Code (Rectangular Graph)

Heads Up for Readers SPAdes vs Ray Benchmarking is Done

Starting to Understand the SPAdes Papers

What are the Puzzle Pieces in a Rectangle Graph?

Rectangular Graph Algorithm

SOAPdenovo

Testing SOAPdenovo2 Pre-release Version

Testing SOAPdenovo2 Pre-release Version II (pregraph_sparse)

Testing SOAPdenovo2 Prelease Version III

Testing SOAPdenovo2 Prerelease IV (building contigs)

Testing SOAPdenovo2 Prerelease V (map and scaff)

Should SOAPdenovo2 Source Code be Made Public?

Our First Look at SOAPdenovo2 Source Code

SOAPdenovo2 Demystified part 1

SOAPdenovo2 Demystified part (a)

January is Our Learn How SOAPdenovo2 Works Month

Our First Look at SOAPdenovo2 Source Code

Should SOAPdenovo2 Source Code be Made Public?

SOAPdenovo2 and Other News from BGI

SOAPdenovo2 Binary is on SourceForge

Testing SOAPdenovo2 Prelease Version III

Testing SOAPdenovo2 Prerelease IV (building contigs)

Testing SOAPdenovo2 Prerelease V (map and scaff)

Testing SOAPdenovo2 Pre-release Version

Testing SOAPdenovo2 Pre-release Version II (pregraph_sparse)

Using SOAPdenovo2 with SOLiD Sequences

Other Assemblers

String Graph Assembler

String Graph of a Genome

High-throughput Microbial Population Genomics using the Cortex Variation Assembler

Working Through the Code of Cortex Variant Assembler

A Comment from Developer of Ray Assembler

A Quantitative Comparison of DNA Sequence Assembly Programs

An Efficient Preprocessing Module for Joining Paired end Reads before Assembly

Various Bioinformatics Programs

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

Paircomp Comparing Two Genomes to Find Conserved cis-regulatory Segments

Paircomp on Steroid (using Bowtie)

CHANCE A Comprehensive and Easy-to-use Software for ChIP-seq QC

Pacbio

A Simulator for Pacbio Reads

HGAp Very Accurate de novo Genome Assembly from PacBio Data

An Update on Using Pacific Bio Sequences for Genome Assembly

Experiments, Libraries

An Elegant Use of NG Sequencing Finding T-cell Diversity

A Great Review of Various Sequencing Instruments/Technologies

Illumina Paired End Libraries Inward and Outwardly Directed Reads

Animations for Sequencing Technologies from the Web

Basic Local Alignment with Successive Refinement (BLASR) for PacBio

Sequencing miRNAs with NGS Technology

Sequencing War and NextEra Kit

Do Illumina and Pacific Bio Fit Together?

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

Excellent Slides from Fisherman Lex on Combining PacBio and Short Reads

HDF5 Data Format for PacBio Sequences

HGAp Very Accurate de novo Genome Assembly from PacBio Data

Mixing Illumina and PacBio Data for Genome Finishing

PACB: This Does not Look Right

Pacific Bio Sequences

The Genome Assembly Process and How Pac Bio can Help

Miscellaneous

On Global Warming

One Sign a Forecast about 21st Century Science/Biology is Wrong

Our Response to Best Practices for Scientific Computing Paper

Our Vision for Biology of 21st Century

Patterns of Three

Study Shows Men are Better than Women in Bioinformatics (p<0.05)

Taking the Eulearian Path

The Best Way to Understand Algorithms

The Chinese Mailman, Who Does not Like to Walk

Thoughts on Anecdotal Science by CTB

Top N Reasons NOT to do a Ph.D. in Bioinformatics/Computational Biology

Traits of a Good Scientist

Tweet or Perish?

We See the Light Source Code Should be Published

What Does BTW Stand for?

Why Core Facility Model Adopted by US Universities is a Bad Model

Presenting an Interesting Exchange. Any Thoughts?

Question for Readers Do You like Homolog.us Blog to Cover the Olympics?

Question for the Readers What is the Convention for Submission of Raw Reads these Days?

Question from a Reader on Studying Bioinformatics

Rage Against the Impact Factor

Severe Abnormalities Found in Fukushima Butterflies

The World of Biological Databases

Thoughts on Anecdotal Science by CTB

Top Bioinformatics Contributions of 2012

Two Thoughtful Comments

What is in the News?

Why Efficiency Matters in Big Data Biology

Ranking of Bioinformatics Journals, Who is at #6?

Should University Professors be Allowed to Use Social Media?

SNP Map of Human Population of Entire World Published

Cars are Powerful, but Driving is Hard to Learn; Ride A Mule to Work Today

CB on ENCODE Embargo

Does Citation-index Count in the Era of Google?

ENCODE paper and Ewan Birneys Interview

Energy the Hidden Cost of NGS Analysis

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

FASTG A New Format for Representing Sequences

Few Quick Comments Regarding the Website

For those Running Core Facilities

For Those Running Core Facilities (part 2)

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

HaploMerger: A Software Tool for Assembling Highly Polymorphic Genomes

How to Download Abstracts of All Biology-related Papers for Text-mining

How Will arxiv.org Work for a Large Consortium Project?

How World Solved its First BigData Problem

Humor Announcement of a New Sequencing Technology

Humor at Professor Browns Expense :)

If You Need Break From Science, Here is US Presidential Debate Homolog.us Edition :)

If You Want to Take Your Bioinformatics Analysis to the Cloud

Improved the Search Routine in Our Website

In Turf Battle for Computational Biology, CTB Fires a Shot

Is 1000 Genome Project an Example of Modern Day Alchemy?

Is Basic Science a Business?

Jay Shendures Presentation at Seattle Sequencing Meetup

More is Different !!

NASA Changes Biology Textbooks Again

NOSQL Databases for Bioinformatics

Notes from Supercomputing Conference (SC12)

Notes on Jay Shendures Seattle Meetup Presentation

Obituary of Nimblegen

On Research Code by Deepak Singh

On Discovery of God Particle

#ngsban How to Implement

Top Five Bioinformatics Innovations of 2012? Contest

A Review of Bioinformatics Blogs

Building an NGS Reference List (de novo assembly category)

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

All About miRNAs

Analysis of NGS miRNA Data a Paired-ended Library

Analysis of NGS miRNA Library an Example

Animals Do not Eat their Own Offsprings

Back on Track, Malware Cleaned

Best Algorithm for Bit Reversal

BGI Model

Big Collection of (bio)Informative Slides from C. Titus Brown

Bioinformatics and Computational Biology same? Si, Si, Si.

Bioinformatics Gangnam Style

Blog Kevins GATTACC World Brings Humor into Bioinformatics

Book Chapter Genome Reconstruction: A Puzzle with a Billion Pieces

Browsers for Viewing NGS Data

Bye bye Python; Enter Haskell

Cargo Cult Science

Cars are Powerful, but Driving is Hard to Learn; Ride A Mule to Work Today

Hardware, FPGA

FPGA-based Hardware Accelerators for NGS Analysis

Bringing New Computing Hardware Architecture to Life

CHREC Slides from Supercomputing Conference

What They Never Teach You in Programming Classes

Periodic Digest Posts

Twelve Developments on 12/12/12

Various Developments 11/26/2012

Various Developments 11/28/2012

Various Developments 11/30/2012

Various Developments in Bioinformatics (12/5/2012)

Various Developments in the Bioinformatics World

Quarterly Growth of Array Express

On learning Bioinformatics

Congratulations to Rayan Chikhi for Finishing Rosalind near Top

On Teaching/Learning Bioinformatics Online Socraticqs, Rosalind

Rosalind Project at Algorithmic Biology Laboratory, St. Petersburg

Simple Examples to Learn Bioinformatics Programming

Software Carpentry Very Good Place to Learn Scientific Programming

Trends

Google Trends Bioinformatics

In our Trends Section

In our Trends Section II

March 2012 Update on GEO Trends (Countries)

SRA Trends March 9, 2012

Explosion of Transcriptome Data on Drosophila

Genomes Published in 2012

More on the World of Biological Databases

Where are Innovative NGS Algorithms Coming from?

Which Next-gen Technologies are Popular?

Transcriptomic Research around the Globe

Hashing

Cuckoo Hashing vs Bloom Filter

Perfect Hash Algorithm of Meraculous Assembler

When is your birthday? (on hashing, sparsehash and murmurhash)

Linear Probing and Power of Two Choices

Using Bloom Filter A Simple Introduction for Bioinformaticians

Data compression/Reduction

Quip paper, CRAM paper and CRAM Tools

Quip, Minia, SlimGene and Titus Browns paper on Scaling Metagenome

Compression of Next-generation Sequencing Reads Aided by Highly Efficient de novo Assembly

Digital Normalization from C. Titus Brown

How to Deal with Massive Sequence Libraries (Slides: CTB)

Informative Slides on the Scale of Data Problem in New Biology

Several Good Posts on Compressing NGS Libraries

Streaming Lossy Compression of Biological Sequence Data using Probabilistic Data Structures

The Beachcombers Dilemma and Diginorm Manual

Legal

How do JGI Data Release Policy and Bleeding Edge Bioinformatics Fit Together?

More on GPL Licensing of Bioinformatics Programs

Software Licenses in Bioinformatics Programs and Their Legal Implications

Humor

NASA Changes Biology Textbooks Again

Nextgen Humor

Very Funny Hitler on IonTorrent Proton

Weekend Humor



Written by M. //