BOL: Related items

Porechop: tool for finding and removing adapters from Oxford Nanopore reads

Rahul Nayak — Tue, 29 May 2018 07:33:44 -0500

Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads. Porechop performs thorough alignments to effectively find adapters, even at low sequence identity.

Porechop also supports demultiplexing of Nanopore reads that were barcoded with the Native Barcoding Kit, PCR Barcoding Kit or Rapid Barcoding Kit.

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

Senior Research Fellow (SRF) Bioinformatics at AIIMS, India

Tue, 04 Aug 2015 03:14:32 -0500

DEPARTMENT OF BIOTECHNOLOGY
ALL INDIA INSTITUTE OF MEDICAL SCIENCES
NEW DELHI-110029

Requirement of Senior Research Fellow Applications are invited for the following vacancy under Research project entitled “Exploiting temporal transcription profile, computational analysis and post-transcriptional gene silencing to identify and intercept interactions between host and dormant and actively replicating Mycobacterium tuberculosis”

Senior Research Fellow One

M.Sc. Degree in Biotechnology/ /Microbiology/Bioinformatics and 2 years research experience in the relevant field NET/GATE Qualification with at least 2 years research experience in M. tuberculosis culture and related techniques as well as transcriptome data generation and analysis.

1 year

1. Age relaxation for SC/ST/OBC/PH Candidates will be as per the government rules.

2. Qualification/degree should be from a reputed Institution/University.

3. Mere fulfilling the essential qualification/experience does not guarantee selection.

4. Canvassing in any form will be a disqualification.

5. No TA/DA will be paid either for attending the interview or joining the post.

Interested candidates are to submit their Curriculum Vitae by 5 PM on 17th August, 2015 to Room No.107, Department of Biotechnology, AIIMS, New Delhi-29.

Only shortlisted candidates will be notified by email for interview

www.aiims.edu/images/pdf/recruitment/advertisement/advertisement%20of%20SRF_N1306.pdf

RNA-seq Analysis Workshop Course Materials

Jit — Tue, 03 Jul 2018 08:14:14 -0500

RNAseq can be roughly divided into two "types": Reference genome-based - an assembled genome exists for a species for which an RNAseq experiment is performed. It allows reads to be aligned against the reference genome and significantly improves our ability to reconstruct transcripts. This category would obviously include humans and most model organisms but excludes the majority of truly biologically intereting species (e.g., Hyacinth macaw); Reference genome-free - no genome assembly for the species of interest is available. In this case one would need to assemble the reads into transcripts using de novo approaches. This type of RNAseq is as much of an art as well as science because assembly is heavily parameter-dependent and difficult to do well. In this lesson we will focus on the Reference genome-based type of RNA seq. http://chagall.med.cornell.edu/RNASEQcourse/

Address of the bookmark: http://chagall.med.cornell.edu/RNASEQcourse/

Bioinformatics Symposium

Tue, 11 Aug 2015 04:02:59 -0500

This 2 day symposium will focus on topics in the below mentioned areas.

Experts from India and Japan in this fields will deliver lectures and contribute in discussions. This will provide an opportunity to the participants to interact and learn.

Topics:

Algorithms for biomolecular Sequences / Structures
Bioinformatics databases and tools
High performance computing
Large scale data analysis
Protein function
Structure based drug design
Applications to specific diseases

More at http://www.iitm.ac.in/bioinfo/Symposium-2015/index.html

AlignQC: A tool for assessing an alignment, and generating reports that are easy to share

Jit — Tue, 07 Aug 2018 04:41:07 -0500

Long read alignment analysis. Generate a reports on sequence alignments for mappability vs read sizes, error patterns, annotations and rarefraction curve analysis. The most basic analysis only requires a BAM file, and outputs a web browser compatible xhtml to visualize/share/store/extract analysis results.

https://f1000research.com/articles/6-100/

https://github.com/jason-weirather/AlignQC

Address of the bookmark: https://www.healthcare.uiowa.edu/labs/au/AlignQC/

Bioinformatics Jokes !!

Jitendra Prajapati — Fri, 21 Aug 2015 01:26:54 -0500

Why was the Bioinformatics fired from his job?

A: He was getting too Sassy.

What did the bioinformatician say when he found out his team stopped using version control?

A: Y’all better Git!

Why did the computational biologist stay home from work?

A: He had a code!

Why was the bioinformatician's paper was rejected?

A: Journal thought it seemed scripted.

How can you tell that a Bioinformatics is working?

A: You can hear him Grunting!

Why bioinformatician always silence?

A: Because bioinformatician calmly whisper, “SSH”

Why was the bioinformatician always so sleepy?

A: He/She wasn’t given any Java.

Why did the program/software hanged?

A: Because genome float.

Why was the class upset that its parent died?

A: Because it wouldn’t be getting the inheritance!

Why did bioinformatician always works on the command line?

A: Because they don't want to scare you with huge amount of data!

Why did the bioinformatician attend the gay pride parade?

A: They supported polymorphism.

Why did bioinformatician prefer awk, PerlOneliner?

A: Because even computer can't handle to load the data.

Why don’t bioinformatician get along with others?

A: They’re too MEAN.

Why computational biologist are cool?

A: Because they are scripted!!

Why they talk $ unzip; strip; touch; finger; grep; mount; fsck; more; yes; fsck; fsck; umount; clean; sleep;

A: Ah, Ohhh, dude, these are *NIX commands

Did they really hack genome?

A: Yes, I guess so.

Platypus: A Haplotype-Based Variant Caller For Next Generation Sequence Data

Shruti Paniwala — Thu, 25 Oct 2018 06:14:55 -0500

Platypus is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data. By using local realignment of reads and local assembly it achieves both high sensitivity and high specificity. Platypus can detect SNPs, MNPs, short indels, replacements and (using the assembly option) deletions up to several kb. It has been extensively tested on whole-genome, exon-capture, and targeted capture data, it has been run on very large datasets as part of the Thousand Genomes and WGS500 projects, and is being used in clinical sequencing trials in the Mainstreaming Cancer Genetics programme.

Tutorial https://github.com/andyrimmer/Platypus/blob/master/misc/README.txt

Address of the bookmark: http://www.well.ox.ac.uk/platypus

Essentials of Statistics and Data Analysis using R

Mon, 31 Aug 2015 01:32:12 -0500

Clinical Development Services Agency (CDSA) is an extramural unit of Translational Health Science and Technology Institute (THSTI), Department of Biotechnology, Ministry of Science & Technology, Government of India. CDSA has a national mandate of strengthening capacity and capability building in the area of Clinical development and Translational Research.

CDSA is pleased to announce a 4 days hands-on training program on “Essentials of Statistics and Data Analysis using R” at ICGEB, Aruna Asaf Ali Road, New Delhi on December 1 – 4, 2015. This will involve developing and enhancing skills to understand basic principles of statistics for summarizing data and use of appropriate statistical tests as well as providing an understanding of data analysis using R. Didactic lectures with practical sessions will be delivered by experienced faculties from AIIMS and Novartis. Live classroom with power point presentations, case studies, mock exercise, practical sessions on R, group work with time for discussion and Q&A sessions are added advantages of this workshop.

Please contact gayatrivishwakarma.cdsa@thsti.res.in or vineetabaloni.cdsa@thsti.res.in for program and registration details.

Please nominate personage or register yourself on or before November 6, 2015 along with the electronic transfer of registration fee.

snakepipes: A toolkit based on snakemake and python for analysis of NGS data

Jit — Thu, 30 May 2019 04:06:13 -0500

snakePipes are flexible and powerful workflows built using snakemake that simplify the analysis of NGS data.

DNA-mapping*
ChIP-seq*
RNA-seq*
ATAC-seq*
scRNA-seq
Hi-C
Whole Genome Bisulfite Seq/WGBS

(*Also available in "allele-specific" mode)

snakePipes can be installed via conda :

'conda install -c mpi-ie -c bioconda -c conda-forge snakePipes'.

Source code (https://github.com/maxplanck-ie/snakepipes) and documentation (https://snakepipes.readthedocs.io/en/latest/) are available online.

Address of the bookmark: https://github.com/maxplanck-ie/snakepipes

gapFinisher: A reliable gap filling pipeline for SSPACE-LongRead scaffolder output

Rahul Nayak — Fri, 24 Jan 2020 06:04:40 -0600

gapFinisher is based on the controlled use of a previously published gap filling tool FGAP and works on all standard Linux/UNIX command lines. They compare the performance of gapFinisher against two other published gap filling tools PBJelly and GMcloser.

gapFinisher can fill gaps in draft genomes quickly and reliably.

Address of the bookmark: https://github.com/kammoji/gapFinisher