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
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
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
Hadoop
Using Hadoop for Transcriptomics - An Example to Get Started
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 - part II
Finding us in homolog.us III (Search Algorithm and Indexing)
Burrows Wheeler transform - Suffix Arrays and FM Index
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
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
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
