BOL: Related items

RNA-Bloom: a fast and memory-efficient de novo transcript sequence assembler

LEGE — Thu, 09 Jul 2020 03:13:06 -0500

RNA-Bloom is a fast and memory-efficient de novo transcript sequence assembler. It is designed for the following sequencing data types:

single-end/paired-end bulk RNA-seq (strand-specific/agnostic)
paired-end single-cell RNA-seq (strand-specific/agnostic)
nanopore RNA-seq (PCR cDNA/direct cDNA/direct RNA)

Written by Ka Ming Nip ✉️

Address of the bookmark: https://github.com/bcgsc/RNA-Bloom

Unicycler: Hybrid assembly pipeline for bacterial genomes

Jit — Fri, 10 Nov 2017 03:58:27 -0600

Unicycler is an assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets where it functions as a SPAdes-optimiser. It can also assembly long-read-only sets (PacBio or Nanopore) where it runs a miniasm+Racon pipeline. For the best possible assemblies, give it both Illumina reads and long reads, and it will conduct a hybrid assembly.

Address of the bookmark: https://github.com/rrwick/Unicycler

Project Scientist at National Agri-Food Biotechnology Institute (NABI)

Thu, 25 Aug 2016 05:49:36 -0500

Advt. No. NABI/8(18)/2012-PME-3
Project Scientist recruitment in National Agri-Food Biotechnology Institute (NABI)
Project Title : “Transfer and Evaluation of Indian Banana with Pro-Vitamin A (PVA) Constructs”
Essential qualifications: Ph.D. thesis submitted/awarded in any branch of life/plant sciences. Desirable qualification: a) Excellent academic record with research experience in area relevant to plant metabolic engineering, molecular biology and bioinformatics supported with high quality publications. b) Knowledge and experience of Chromatography and Mass Spectrometry based technological analysis of samples. c) Knowledge and experience of in-silico analysis such as trascriptomics, proteomics and genomics. c) Relevant research publications in reputed international journals with high impact factors.
No. of Post : 01
Age: 35 years
Emoluments: Rs.40,000/- per month.
How to apply
Walk-In-Interview on 29/08/2016 at National Agri-Food Biotechnology Institute, C-127, Industrial Area, Phase VIII, S.A.S. Nagar, Mohali-160 071 Email: siddharth@nabi.res.in

More at http://www.nabi.res.in/Vacancies/NABI/ResearchFellowships/JRFSRFRA/2016/NABI8(18)2012-PME-3/Advt.pdf

Traineeship/Studentship conducts University of Delhi (Gargi College)

Mon, 05 Sep 2016 03:45:58 -0500

Traineeship/Studentship cunducts University of Delhi (Gargi College) on purely temporary for a period of six months.
Traineeship — 01 (one post)
Essential Qualification: Post Graduate degree in Bioinformatics or any other branch of Life Sciences preferably with dissertation in Bioinformatics. Desirable Qualification: Prior knowledge of programming languages such as C, VB, SQL etc. and software/database development
Studentship- 01 (one post)
Essential Qualifications: Final year Post Graduate students pursuing a degree in Bioinformatics or any branch of Life Science with knowledge of bioinformatics
Salary: Rs.8000/- p.m.
How to apply
Interested candidates are required to appear for the walk in interview on 14th. September, 2016 at 9.30 AM in Principal's Office, Gargi College, Sirifort Road, N. Delhi-110049

More at http://www.du.ac.in/du/index.php?mact=News,cntnt01,detail,0&cntnt01articleid=12859&cntnt01returnid=83

ASplice: a scalable and memory-efficient algorithm for de novo transcriptome assembly

Rahul Nayak — Tue, 03 Jul 2018 04:09:46 -0500

With increased availability of de novo assembly algorithms, it is feasible to study entire transcriptomes of non-model organisms. While algorithms are available that are specifically designed for performing transcriptome assembly from high-throughput sequencing data, they are very memory-intensive, limiting their applications to small data sets with few libraries. Texas A&M University researchers develop a transcriptome assembly algorithm that recovers alternatively spliced isoforms and expression levels while utilizing as many RNA-Seq libraries as possible that contain hundreds of gigabases of data. New techniques are developed so that computations can be performed on a computing cluster with moderate amount of physical memory. Availability – A software program that implements the algorithm is available at: http://faculty.cse.tamu.edu/shsze/asplice. Sze SH, Pimsler ML, Tomberlin JK, Jones CD, Tarone AM. (2017) A scalable and memory-efficient algorithm for de novo transcriptome assembly of non-model organisms. BMC Genomics 18(Suppl 4):387.

Address of the bookmark: http://faculty.cse.tamu.edu/shsze/asplice/

MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph

Jit — Wed, 14 Nov 2018 04:50:27 -0600

MEGAHIT is a single node assembler for large and complex metagenomics NGS reads, such as soil. It makes use of succinct de Bruijn graph (SdBG) to achieve low memory assembly. MEGAHIT can optionally utilize a CUDA-enabled GPU to accelerate its SdBG contstruction. The GPU-accelerated version of MEGAHIT has been tested on NVIDIA GTX680 (4G memory) and Tesla K40c (12G memory) with CUDA 5.5, 6.0 and 6.5. MEGAHIT v1.0 or greater also supports IBM Power PC and has been tested on IBM POWER8.

https://academic.oup.com/bioinformatics/article/31/10/1674/177884

Address of the bookmark: https://github.com/voutcn/megahit

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

NxRepair: error correction in de novo assemblies using Nextera Mate Pair Reads

BioStar — Thu, 24 Jan 2019 10:35:12 -0600

NxRepair is a python module that automatically detects large structural errors in de novo assemblies using Nextera mate pair reads. The decector will break a contig at the site of an identified misassembly and will generate a new fasta file containing both the corrected contigs and the correct, unaffected contigs.

https://nxrepair.readthedocs.io/en/latest/tutorial.html

nxrepair aligned_matepairs.bam assemblyfasta.fasta error_locations.csv new_fasta.fasta

Address of the bookmark: https://github.com/rebeccaroisin/nxrepair

SDA: Long-read sequence and assembly of segmental duplications

Jit — Tue, 05 Mar 2019 10:00:57 -0600

Segmental Duplication Assembler (SDA; https://github.com/mvollger/SDA) constructs graphs in which paralogous sequence variants define the nodes and long-read sequences provide attraction and repulsion edges, enabling the partition and assembly of long reads corresponding to distinct paralogs.

https://github.com/mvollger/SDA

Address of the bookmark: https://www.nature.com/articles/s41592-018-0236-3