BOL: Related items

Integrative Genomics Viewer (IGV) tutorial

Neel — Sat, 12 Jul 2014 15:16:23 -0500

The Integrative Genomics Viewer (IGV) from the Broad Center allows you to view several types of data files involved in any NGS analysis that employs a reference genome, including how reads from a dataset are mapped, gene annotations, and predicted genetic variants.

http://www.broadinstitute.org/igv/

Address of the bookmark: https://wikis.utexas.edu/display/bioiteam/Integrative+Genomics+Viewer+%28IGV%29+tutorial

COSMOS, our workflow management system for NGS data

Jit — Wed, 23 Jul 2014 07:29:14 -0500

COSMOS, our Python-based management system for implementing large-scale parallel workflows focusing on, but not restricted to, large-scale short-read "NGS" sequencing data is open-access published via Advance Access in Bioinformatics (Gafni et al. 2014). It is also available for download for non-commercial academic and research purposes at:

http://cosmos.hms.harvard.edu/.

Address of the bookmark: https://cosmos.hms.harvard.edu/

Swabs to Genomes: A Comprehensive Workflow

Rahul Nayak — Sun, 10 Aug 2014 03:01:21 -0500

The sequencing, assembly, and basic analysis of microbial genomes, once a painstaking and expensive undertaking, has become almost trivial for research labs with access to standard molecular biology and computational tools. However, there are a wide variety of options available for DNA library preparation and sequencing, and inexperience with bioinformatics can pose a significant barrier to entry for many who may be interested in microbial genomics. The objective of the present study was to design, test, troubleshoot, and publish a simple, comprehensive workflow from the collection of an environmental sample (a swab) to a published microbial genome; empowering even a lab or classroom with limited resources and bioinformatics experience to perform it.

Address of the bookmark: https://peerj.com/preprints/453.pdf

Bioinformatics WalkIn at NII

Fri, 04 Sep 2015 21:48:15 -0500

ADVERTISEMENT OF WALK-IN-INTERVIEW

NAME OF THE POST : Bioinformatician (Part time 3 days in a week) (One Position only)

DURATION : One Year

NAME OF THE PROJECT : Next generation sequencing facility

EDUCATIONAL QUALIFICATIONS : At least a Masters degree in Bioinformatics and Bachelors degree in any stream of life sciences

REQUIREMENTS :

Around 5 years of experience and proven track record in next generation sequence data analysis (supported by publications in peer-reviewed journals), ability to analyze transcriptomics, Chip-seq, and small RNA –seq data.

: Should have the ability to analyze raw primary data generated by Illumina next generation sequencing platforms and create / troubleshoot custom analysis Pipelines.

Should have ability to handle all downstream secondary and tertiary data analysis using commercially available as well as open source softwares (transcriptomics, ChIP-seq, small RNA-seq)

Apart from these, the applicant should have knowledge of the following: Programming: Perl and Python. Operating system:

Linux and Windows. NGS Analysis tools: Maq, BWA, Bowtie, SAM tools, BEDTools, MACS, Galaxy, FastQC, Bismark, MEDIPS, Tophat, Cufflinks, AvadisNGS, CLC Genomics Workbench, Galaxy, BaseSpace, Trinity Statistics: Microsoft Excel and R. Database: MySQL Genome Browser: UCSC, Ensemble, IGV, IGB Motif Analysis Tools: MEME Suite, Transfac and RSAT Functional Annotation Tools: DAVID, GeneCodis, Gene Cards Networking Tools: Cytoscape

EMOLUMENTS : The incumbent will be paid a fee of Rs. 2000/- per sitting/ per day.

SCIENTIST NAME : Dr. Arnab Mukhopadhyay,

Staff Scientific V Next generation sequencing facility

SCIENTIST’S E-MAIL ID : arnab@nii.ac.in

WALK IN INTERVIEW ON : 18th September, 2015

REGISTRATION OF CANDIDATES: 10.30 AM to 11.00 AM

PLEASE NOTE- 1. CANDIDATE MAY FILL UP APPLICATION IN THE PRECRIBED FORMAT ALONG WITH NECESSARY DOCUMENTS FOR VERIFICATION. 2. APPLICATIONS CONTAINING INCOMPLETE INFORMATION SHALL NOT BE ENTERTAINED. 3. DATE OF PASSING THE EXAMINATIONS MUST BE INDICATED CLEARLY. 4. ONLY REGISTERED CANDIDATES WILL BE INTERVIEWED. 5. NO TA/DA WILL BE PAID FOR ATTENDING THE INTERVIEW PRESCRIBED FORM 1. NAME 2. FATHER’S NAME 3. MOTHER’S NAME 4. DATE OF BIRTH 5. SEX (MALE/FEMALE) 6. CATEGORY (SC/ ST/ OBC/ PH) 7. ADDRESS a. (CORRSPONDENCE) b. (PERMANENT) 8. E MAIL, TELEPHONE NO. & MOBILE No (if any) 9. ACADEMIC & PROFESSIONAL QUALIFICATIONS NAME OF EXAMINATION PASSED WITH SUBJECTS YEAR OF PASSING BOARD/ UNIVERSITY PERCENTAGE/ DIVISION REMARKS 10. PAST EXPERIENCE & PRESENT EMPLOYMENT, IF ANY 11. CANDIDATES SHOULD STATE CLEARLY WHETHER THEY HAVE BEEN AWARDED PH.D DEGREE OR THESIS HAS BEEN SUBMITTED. 12. HAVE YOU APPLIED FOR A POSITION EARLIER IN THE INSTITUTE? IF SO:- (1) THE DETAILS OF THE PROJECT AND PROJECT INVESTIGATOR (2) IF CALLED FOR INVERVIEW, RESULTS THEREOF

More at http://www1.nii.res.in/sites/default/files/walkininterview-18sept2015.pdf

HiCdat

Jit — Fri, 12 Feb 2016 05:23:44 -0600

HiCdat: a fast and easy-to-use Hi-C data analysis tool

HiCdat is easy-to-use and provides solutions starting from aligned reads up to in-depth analyses. Importantly, HiCdat is focussed on the analysis of larger structural features of chromosomes, their correlation to genomic and epigenomic features, and on comparative studies. It uses simple input and output formats and can therefore easily be integrated into existing workflows or combined with alternative tools.

More at http://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0678-x

Address of the bookmark: https://github.com/MWSchmid/HiCdat

UCSC Genome Browser and Blat software !

Jit — Thu, 18 Feb 2016 03:18:57 -0600

This directory contains Genome Browser and Blat application binaries built for standalone
command-line use on various supported Linux and UNIX platforms. To determine which set of binaries
to download, type "uname -a" on the command line to display your machine type. In most cases the
usage statement for the application can be viewed by running the binary with no arguments.

The UCSC Genome Browser and Blat software are free for academic, nonprofit, and personal use. A
license is required for commercial download and installation of these binaries, with the exception
of items built from the following source code directories, which are freely available for all uses:

- kent/src/utils (includes big* tools)
- kent/src/lib
- kent/src/hg/autoSql
- kent/src/hg/autoXml

For information about commercial licensing of the Genome Browser software, see
http://genome.ucsc.edu/license/. The Blat and In-Silico PCR software may be commercially
licensed through Kent Informatics (http://www.kentinformatics.com).

More at http://hgdownload.cse.ucsc.edu/admin/exe/

Address of the bookmark: http://hgdownload.cse.ucsc.edu/admin/exe/

Machine Learning !!!

Gudiya Pal — Fri, 01 Jul 2016 12:57:12 -0500

In machine learning, computers apply statistical learning techniques to automatically identify patterns in data. These techniques can be used to make highly accurate predictions.

Keep scrolling. Using a data set about homes, we will create a machine learning model to distinguish homes in New York from homes in San Francisco.

Address of the bookmark: http://www.r2d3.us/visual-intro-to-machine-learning-part-1/

Efficient genome searching with Biostrings and the BSgenome data package

Aasha — Mon, 07 Mar 2016 05:18:06 -0600

Address of the bookmark: https://www.bioconductor.org/packages/3.3/bioc/vignettes/BSgenome/inst/doc/GenomeSearching.pdf

SCALCE

Surabhi Chaudhary — Fri, 15 Apr 2016 05:09:51 -0500

SCALCE (/skeɪlz/, a.k.a. boosting Sequence Compression Algorithms using Locally ConsistentEncoding) is a tool for compressing FASTQ files. It is designed specifically for the Illumina-generated FASTQ files, but supports any valid FASTQ with consistent read lengths.

More at http://sfu-compbio.github.io/scalce/

Address of the bookmark: http://sfu-compbio.github.io/scalce/

MEDEA: Comparative Genomic Visualization with Adobe Flash

Jit — Tue, 26 Apr 2016 12:15:16 -0500

As the number of sequence and annotated genomes grows larger, the need to understand, compare, and contrast the data becomes increasingly important. Using the power of the human visual system to detect trends and spot outliers is necessary in such large and complex data sets.

More at http://www.broadinstitute.org/annotation/medea/

Address of the bookmark: http://www.broadinstitute.org/annotation/medea/