BOL: Related items

Artemis Comparison Tool (ACT)

Shruti Paniwala — Wed, 07 Sep 2016 03:54:41 -0500

ACT is a Java application for displaying pairwise comparisons between two or more DNA sequences. It can be used to identify and analyse regions of similarity and difference between genomes and to explore conservation of synteny, in the context of the entire sequences and their annotation. It can read complete EMBL, GENBANK and GFF entries or sequences in FASTA or raw format.

Address of the bookmark: http://www.sanger.ac.uk/science/tools/artemis-comparison-tool-act

CIRCOS Visualize !!

Jit — Fri, 02 Sep 2016 08:29:26 -0500

Before uploading a data file, check the samples gallery to make sure that your data format is compatible.

Your file must be plain text.
Your data values must be non-negative integers.
Data must be space-separated (one or more tab or space, which will be collapsed).
No two rows or columns may have the same name.
Column and row names must begin with a letter (e.g. 'A', 'A0', 'A-0') and can only contain letters, numbers and _. No punctuation!
Maximum row + column total is 150 — if exceeded, rows and columns are limited to 75.
If you are using order, size and color rows/columns in combination they must appear in that order.

Need help? Post questions to the Circos Google Group.

http://mkweb.bcgsc.ca/tableviewer/visualize/

Address of the bookmark: http://mkweb.bcgsc.ca/tableviewer/visualize/

Structural variants PPT

Jit — Wed, 07 Sep 2016 03:16:09 -0500

1000 Genomes data tutorial at ASHG

Structural variants presentation by

Jan Korbel

European Molecular Biology Laboratory (EMBL) Heidelberg Genome Biology Research Unit

Reference:

https://www.genome.gov/pages/research/der/1000genomesprojecttutorials/structuralvariants-jankorbel.pdf

FERMI

Jit — Fri, 09 Sep 2016 05:37:13 -0500

Fermi is a de novo assembler with a particular focus on assembling Illumina short sequence reads from a mammal-sized genome. In addition to the role of a typical assembler, fermi also aims to preserve heterozygotes which are often collapsed by other assemblers. Its ultimate goal is to find a minimal set of
unitigs to represent all the information in raw reads.

Fermi follows the overlap-layout-consensus paradigm and uses the FM-DNA-index (FMD-index) as the key data structure. It is inspired by the string graph assembler (Simpson and Durbin, 2010 and 2012) and has a similar workflow.

As a typical de novo assembler, fermi tends to produce contigs with slightly longer N50. However, the major weakness of fermi is the high misassembly rate. Although fermi provides a tool to fix misassemblies by using paired-end reads to achieve an accuracy comparable to other assemblers, this is not a favorable solution.

Fermi is designed to be used on a multi-core Linux machine with large shared memory. The easiest way to run fermi is to use the run-fermi.pl script. It generates a Makefile. The actual assembly is done by invoking make. Premature assembly processes can be resumed. Here is an example:

run-fermi.pl -dAPe ./fermi -p NA12878 -t16 -f18 reads*.fq.gz > NA12878.mak
make -f NA12878.mak -j16

Address of the bookmark: https://github.com/lh3/fermi

SRF Bioinformatics at Bose Institute, India

Thu, 29 Sep 2016 09:39:13 -0500

Advt. No. S/DPB(CB)/17/2016-17
Junior Research Assistant/ Senior Research Assistant Job vacancies in Bose Institute on temporary basis
Project Title : “Genome wide transcriptome analysis to identity MYMIV-stress related genomic resources of blackgram”
Junior Research Assistant
Qualification : Good academic record in B.Sc. and M.Sc. in Botany or Biotechnology from reputed Universities. Must have good practical hand, this should be certified by two Senior/reputed PG teachers on a scale of 10.
Desirable : Preference will be given to those who already have some research experience (for at least 2 months).
Consolidated Pay : Rs. 16,400/- p.m.
Age Limit : Below 28 years (relaxable in case of SC/ST/OBC/Women candidates only as per rules).
Senior Research Assistant
Qualification : B.Sc. in Biotechnology and M.Sc. in Biotechnology or Bioinformatics. Hands on training in Bioinformatics. At least two Research Publications with Bioinformatics components.
Desirable : Preference will be given to the candidates who have previous experience in Next Gen Sequencing data analysis of genomic/transcriptome/miRNA.
Consolidated Pay : Rs. 18,700/- p.m.
Age Limit : Below 30 years (relaxable in case of SC/ST/OBC/Women candidates only as per rules).

http://www.boseinst.ernet.in/advertisement.html

Murasaki

Anjana — Fri, 30 Sep 2016 10:22:30 -0500

Murasaki is an anchor alignment program that is

exteremely fast (17 CPU hours for whole Human x Mouse genome (with 40 nodes: 35 wall minutes), or 8 mammals in 21 CPU hours (42 wall minutes))
scalable (Arbitrarily parallelizable across multiple nodes using MPI)
memory efficient. (Even a single node with 16GB of ram can handle over 1Gbp of sequence)
unlimited by pattern length or selection
repeat tolerant

Address of the bookmark: http://murasaki.dna.bio.keio.ac.jp/wiki/index.php?Murasaki

MIRO : miRNA omics

Jit — Tue, 04 Oct 2016 14:50:48 -0500

The MIRO (the miRNA omics) pipeline is a flexible and powerful tool for the analysis of miRNA (or more generall short RNA) expression using short-read deep sequencing data. In its present implementation MIRO is especially adapted for the analysis of reads generated with the Illumina sequencing platform. MIRO allows to preprocess the Solexa-reads, map them flexibly to several reference genomes using one of four different mappers, create differential gene (miRNA) expression profiles and cluster reads using one of several algorithm. MIRO output is furthermore compatible with software such as genome browsers and miRDeep.

Address of the bookmark: http://seq.crg.es/download/software/Miro/

How to install Perl modules on Mac OS X in easy steps !!

Jit — Thu, 20 Oct 2016 07:26:29 -0500

Today at work, I learned how to install Perl modules using CPAN. It’s a lot easier than I thought.

You see, for the past couple of years, I’ve been a bit frustrated because OS X does not come with a whole lot of Perl modules pre-installed, and for all I googled, I couldn’t find an “idiot’s” guide for moderately-savvy-but-not-expert users like myself to install modules and dependencies on demand.

The only instructions I could find point to Fink, which basically installs modules in a path that isn’t included in the Perl @INC variable, meaning you have to manually specify the full path to the modules in every script — which is not a lot of fun if you’re developing on OS X and deploying on Red Hat, for instance.

Moreover, Fink doesn’t seem to make every module available, and it’s not very easy to determine which Fink package you need to install if you need a particular module.

So, with a script that called on several apparently unavailable modules, and a deadline looming, I finally decided to suck it up and figure out how to use CPAN to install them:

1) Make sure you have the Apple Developer Tools (XCode) installed.

These are on one of your install discs, or available as a huge but free download from the Apple Developer Connection [free registration required] or the Mac App Store. I thought I had them, but apparently when we upgraded that computer to Tiger, they went missing.

If you don’t have this stuff installed, your installation will fail with errors about unavailable commands.

1.5) Install Command Line Tools (Recent XCode versions only)

(Thank you to Tom Marchioro for informing me about this step.)

Older versions of XCode installed the command line tools (which are required to properly install CPAN modules) by default, but apparently newer ones do not. To check whether you have the command line tools already installed, run the following from the Terminal:

$ which make

This command checks the system for the “make” tool. If it spits out something like /usr/bin/make you’re golden and can skip ahead to Step 2. If you just get a new prompt and no output, you’ll need to install the tools:

Launch XCode and bring up the Preferences panel.
Click on the Downloads tab
Click to install the Command Line Tools

If you like, you can run which make again to confirm that everything’s installed correctly.

2) Configure CPAN.

$ sudo perl -MCPAN -e shell

perl> o conf init

This will prompt you for some settings. You can accept the defaults for almost everything (just hit “return”). The two things you must fill in are the path to make (which should be /usr/bin/make or the value returned when you run which make from the command line) and your choice of CPAN mirrors (which you actually choose don’t really matter, but it won’t let you finish until you select at least one). If you use a proxy or a very restrictive firewall, you may have to configure those settings as well.

If you skip Step 2, you may get errors about make being unavailable.

3) Upgrade CPAN

$ sudo perl -MCPAN -e 'install Bundle::CPAN'

Don’t forget the sudo, or it’ll fail with permissions errors, probably when doing something relatively unimportant like installing man files.

This will spend a long time downloading, testing, and compiling various files and dependencies. Bear with it. It will prompt you a few times about dependencies. You probably want to enter “yes”. I agreed to everything it asked me, and everything turned out fine. YMMV of course. If everything installs properly, it’ll give you an “OK” at the end.

4) Install your modules. For each module….

$ sudo perl -MCPAN -e 'install Bundle::Name'

$ sudo perl -MCPAN -e 'install Module::Name'

This will install the module and its dependencies. Nice, eh? Again, don’t forget the sudo.

The first time you run this after upgrading CPAN, it may prompt you to configure again (see Step 2). If you accept its offer to try to configure itself automatically, it may just run through everything without a problem.

There are a couple of potential pitfalls with specific modules (such as theLWP::UserAgent / HEAD issue), but most have workarounds, and I haven’t run into anything that wasn’t easily recoverable.

And that’s it!

Did you find this useful? Is there anything I missed?

Traineeship at JAWAHARLAL NEHRU TROPICAL BOTANIC GARDEN AND RESEARCH INSTITUTE

Fri, 25 Nov 2016 08:07:59 -0600

JAWAHARLAL NEHRU TROPICAL BOTANIC GARDEN AND RESEARCH INSTITUTE

THIRUVANANTHAPURAM - 695 562

Traineeship on Bioinformatics(2)

First class M.Sc. Bioinformatics/ Agriculture/ Botany/ Biotechnology @ Rs.8000

Those candidates who fulfill the above criteria may attend a walk PCC Coordinator in-interview on 28th November 2016 at Saraswathy Thangavelu center, JNTBGRI, Puthenthope, Thiruvananthapuram between at 10.00 am and 2.00 pm with all the relevant document and testimonials.

No TA/DA will be given to candidates for attending the interview.

More Info : http://jntbgri.res.in/downloads/traineeship_notification.pdf

Graph Genome Suite

Jit — Fri, 28 Oct 2016 07:59:54 -0500

Seven Bridges is the biomedical data analysis company accelerating breakthroughs in genomics research for cancer, drug development and precision medicine. We build self-improving systems to analyze millions of genomes, including the Graph Genome Suite — the most advanced population genomics tools in the world.

Address of the bookmark: https://www.sbgenomics.com/graph/