3rd International Whale Shark Conference

The conference web site is here.

Tools for NGS analysis - fastq file processing

As I have recently been working (although very slowly) in person on output of the HiSeq1500 in our facility, I needed to look for, test and validate some tools to handle fastq files for various purposes. Below I list some of them for those who are starting or will start this sort of work.


For various kinds of filtering/trimming

seqtk - a fixed version that retains full sequence names (or 'comments') is here
                      [see a post at BioStar]

fastx-tools (of many tools therein, I am using fastx_trimmer and fastq_quality_filter)

prinseq (of many options, I use 'trim_left/right' and 'derep')

condetri - ... I could not get this working in the way I wanted


For merging overlapping paired-end reads

cope

See this external blog post (from Nov. 2012) for more info


For removing adaptor sequences etc.

tagdust

cutadapt - Can't this tool accept multiple adapter sequences in a multifasta file?


For retrieving paired reads after read filtering

cmpfastq_pe


For removing 'duplicates'

filterPCRdupl (I will not use this any more because 'prinseq -derep 4' does the exactly the same thing much faster)


For validating the tools' functions

fastqc [ also, a tutorial movie available at YouTube ]

fastx_quality_stats

prinseq -stats_all


There should be more useful tools that I did not list here. Please first google with some key words and look into the 'Bioinformatics' forum at SEQanswers to get latest info. Its Wiki page there also provides a list of tools.

International meeting at CDB

The meeting website is here .

Complicated! - lamprey genome resource availability

I have been asked by many of people around me about publicly available resources of the sea lamprey genome. I have just written down some facts and information on an independent new page inside this blog, titled 'Lamprey genome guide'. The situation is somewhat complicated, I see.

I will try to keep this page updated for the lamprey researchers' convenience.
I believe this third-party guide does not interfere any database function and research activity by other researchers. But, please let me know if there is some problem.

'aLeaves' launched !

My team has launched a new tool 'aLeaves' to allow researchers to collect sequences that are homologous to a query (with NCBI Blast). The motivation to launched it is visualized in an image below. I hope it leads to wider uses of molecular phylogenetics and better understanding about how sequences evolve and how gene families have diversified. I would appreciate any feedback from users of this tool.

Indo-Pacific Fish Conference (IPFC)

9th Indo-Pacific Fish Conference (IPFC) is going to be held in Okinawa in June 2013.

Bioinformatician position advertised!

My unit is looking for an individual skilled with large-scale sequence data handling.

The detail is found here:
http://seqanswers.com/forums/showthread.php?t=23818

http://www.nature.com/naturejobs/science/jobs/286326-A-bioinformatician-postdoc-or-technical-staff-at-sequencing-core-unit-of-RIKEN-Center-for-Developmental-Biology

Please feel free to contact to the email address therein for questions etc.

Recent addition to my collection

After I moved to Japan in early Spring, I visited aquarium parks in Japan several times. The most impressive one was that in Okinawa, Churaumi Aquarium.

The newest one I visited was that in Tokyo, Sumida Aquarium. This one was just opened in May 2012, beside the Tokyo Skytree also just opened at the same time.

The below are the miniature figures I bought in the souvenir shop in the Sumida Aquarium. On the left you see the zebra shark (Stegostoma fasciatum), and on the right, the leopard shark (Triakis semifasciata).

The one on the right is my favorite. I didn't expect that I can find figures for these species at all. I got very excited and ended up with spending two thousand yen for them.

EEA 2012 in Milan, Italy

European Elasmobranch Association’s 16th Annual Conference will be held in Milan, Italy, 22th-25h November 2012. [ conference web site ]

My education restarted - Day 1

About 6 months after I quited working in a university in Southern Germany, I gave the first lecture in front of students this week. It was part of the 1-week-long undergrad internship program that the institute hosted. I had students raise their hands for several questions.

They included a basic question, 'Have you had any bioinformatics lecture in your university study?'

Out of 23 very keen students (primarily interested in developmental biology, though), .......................... only 3 raised their hands.

It will take time, but I have to seriously think about how to change this reality.

History to make ... - from Olympic games

I am quietly excited about the rise of Japanese soccer - both mens' and womens'. I did not imagine that the day like this really comes. But, what is really new and what has changed? In my sense, nothing really. Especially, in the mens' team, there is not a single special player. They just have unity, patience and skills. These elements are also what I truly respect in my work, especially in what I am now trying to achieve in my new position in Japan.

Nonsense to compare, but ...

I always get puzzled when I am asked 'which do you like, life in Germany or Japan?'. But, I can easily list differences between them.

On the other hand, there are many things that I previously did not take as advantage of living in Japan. New discoveries!! One of them is that I can access to every kind of research expertise in the country because many, many people live in the small islands (=Japan).

When I was in southern Germany, I felt that I was in the middle of many pretty cities with various research centers and researchers in Switzerland, France, Austria, and of course Germany. But, in fact they were scattered throughout the vast land.

Here in Japan, in the small islands, we have access to all kinds of things, and that is convenient. But, this is the reason why the country tends (or I should say 'we tend'?) to become isolated from the rest of the world. I am seeing all the pros and cons of this tendency.

from Yokohama

Skate genome resource

The journal DATABASE published an article about skate genome annotation. It includes links to the project website and sequence resources .

6 - 0 for Japan

The match between Japan and Jordan was played in Saitama, Japan. The number 10 of the Japanese team, Shinji Kagawa, is moving to Manchester United after scoring 13 goals this year for Borussia Dortmund (BVB!) in Germany. He also scored one goal tonight.

RIKEN CDB Graduate School Guidance

On May 26th, RIKEN CDB in Kobe, Japan, will hold the first annual guidance session for students who want to start developmental biology research for master or doctor program.

Because targeted participants are probably already in Japan, I paste below the official advertisement written in Japanese. I will also join this event and introduce my unit.

----

神戸にある理研 発生・再生総合研究センター（CDB）では、５月２６日（土曜午後）に連携大学院説明会を開くことになりました。http://www.cdb.riken.jp/daigakuin/

この説明会は、理研 発生・再生総合研究センター（CDB）中で、大学院の講座として、大学院生も行ける研究室を紹介しようというもので、今年が初めての試みです。遠隔地からも参加してもらえるよう、午後１２時５０分から開始します。CDBを代表するサイエンティストのレクチャーや連携大学院の教員を兼ねているラボの訪問の機会ももうけてあります（プラス懇親会）。

大学院を決めようとしている学部学生（４年）と修士の学生に広くこの説明会の存在を知ってもらいたいので、mailing list, twitter、facebookを使っている方、あるいは、みなさんのラボの後輩や、そのまた後輩の学部学生に、この情報を伝えていただければ大変ありがたく思います。

ぜひよろしくお願いします。