BOL: Related items

List of bioinformatics packages for NGS analysis !

Rahul Nayak — Sat, 20 Mar 2021 00:28:51 -0500

Package suites gather software packages and installation tools for specific languages or platforms. We have some for bioinformatics software.

Bioconductor – A plethora of tools for analysis and comprehension of high-throughput genomic data, including 1500+ software packages. [ paper-2004 | web ]
Biopython – Freely available tools for biological computing in Python, with included cookbook, packaging and thorough documentation. Part of the Open Bioinformatics Foundation. Contains the very useful Entrez package for API access to the NCBI databases. [ paper-2009 | web ]
Bioconda – A channel for the conda package manager specializing in bioinformatics software. Includes a repository with 3000+ ready-to-install (with conda install) bioinformatics packages. [ paper-2018 | web ]
BioJulia – Bioinformatics and computational biology infastructure for the Julia programming language. [ web ]
Rust-Bio – Rust implementations of algorithms and data structures useful for bioinformatics. [ paper-2016 ]
SeqAn – The modern C++ library for sequence analysis.

Linux for bioinformatician !!!

Rahul Nayak — Thu, 13 Mar 2014 16:59:26 -0500

Linux, free operating system for computers, provides several powerful admin tools and utilities which will help you to manage your systems effectively and handle huge amount of genomic/biological data with an ease. The field of bioinformatics relies heavily on Linux-based computers and software. Although most bioinformatics programs can be compiled to run. If you don’t know what these no so user-friendly tools are and how to use them, you could be spending lot of time trying to perform even the basic admin tasks. The focus of this linux series is to help you understand system admin as well as basic tools, which will help you to become an effective bioinformatician and computational biologist.

For knowledge about Linux and their importance amongst bioinformatician plesae read this article "An introduction to Linux for bioinformatics" by Paul Stothard.

Linux cheat sheet at http://bioinformaticsonline.com/file/view/87/linux-cheat-sheet

Please browse for futher useful linux pages on right hand side ...

Troyanskaya Lab

Tue, 04 Feb 2020 06:40:36 -0600

The goal of our research is to interpret and distill this complexity through accurate analysis and modeling of molecular pathways, particularly those in which malfunctions lead to the manifestation of disease. We are inventing integrative methods for systems-level pathway modeling through integrative analysis of genome-scale datasets. We apply these approaches in studying challenging biological problems, such as how pathways function in diverse cell types and how they change dynamically.

https://function.princeton.edu/

Frequent parameters for bioinformatics tools !

BioStar — Tue, 27 Oct 2020 19:42:32 -0500

Third party executable parameters and options.

Trimmomatic

“ILLUMINACLIP:...:2:30:10”

“LEADING:15”

“TRAILING:15”

“SLIDINGWINDOW:4:20”

“MINLEN:20”

“TOPHRED33”

Filtlong

--min_length 500

--min_mean_q 85

--min_window_q 65

FastQ Screen

--aligner bowtie2' (bwa for PacBio)

--subset 1000 (for PacBio)

SPAdes

--careful

--disable-gzip-output

--cov-cutoff auto

--phred-offset 33

HGAP

Pbalign.task_options.min_accuracy: 70

Pbalign.task_options.no_split_subreads: false

Genomic_consensus.task_options.min_confidence: 40

falcon_ns.task_options.HGAP_GenomeLength_str:

6000000

Pbcoretools.task_options.read_length: 0

Genomic_consensus.task_options.use_score: 0

Pbalign.task_options.min_length: 50

Pbalign.task_options.algorithm_options: --minMatch 12

--bestn 10 --minPctSimilarity 70.0

Pbalign.task_options.hit_policy: randombest

Pbcoretools.task_options.other_filters: rq >= 0.7

Pbalign.task_options.concordant: false

Genomic_consensus.task_options.min_coverage: 5

falcon_ns.task_options.HGAP_SeedCoverage_str: 30

falcon_ns.task_options.HGAP_AggressiveAsm_bool: false

Genomic_consensus.task_options.algorithm: best

falcon_ns.task_options.HGAP_SeedLengthCutoff_str: -1

Genomic_consensus.task_options.diploid: false

MeDuSa

-random 100

Prokka

--usegenus

--force

--addgenes

--rfam

--rawproduct

cmsearch (taxonomy, 16S)

--rfam

--noali

blastn (taxonomy, 16S)

-evalue 1E-10

blastn (MLST)

-ungapped

-dust no

-evalue 1E-20

-word_size 32

-culling_limit 2

-perc_identity 95

blastp (VF)

-culling_limit 2

RGI (ABR)

--input_type contig

bowtie2 (mapping)

--sensitive

minimap2 (mapping)

-a

-x map-ont

samtools mpileup (SNP detection)

-uRI

bcftools call (SNP detection)

--variants-only

--skip-variants indels

--output-type v

--ploidy 1

-c

SNPsift filter (SNP detection)

"( QUAL >= 30 ) & (( na FILTER ) | (FILTER = 'PASS')) &

( DP >= 20 ) & ( MQ >= 20 )"

SNPeff ann (SNP detection)

-nodownload

-no-intron

-no-downstream

-no SPLICE_SITE_REGION

-upDownStreamLen 250

bcftools consensus

(phylogenetic tree)

--haplotype 1

fasttreemp

-nt

-boot 100

roary

-e

-n

-cd 100

-g 100000

Fellowship (Doctoral Research In Biomedical Genomics, Including Statistical Genomics)

Sun, 20 Dec 2015 06:03:43 -0600

Fellowship (Doctoral Research In Biomedical Genomics, Including Statistical Genomics)
Eligibility : MSc(Bio-Chemistry, Bio-Informatics, Bio-Tech, Mathematics / Applied Mathematics, Stati, Zoology)
Location : Kolkata
Last Date : 31 Dec 2015
Hiring Process : Written-test

NO: 340/ESTB/ADMN/NIBMG/2015-16
Doctoral Research In Biomedical Genomics, Including Statistical Genomics conduct National Institute of Biomedical Genomics (NIBMG)
Information For Students Interested To Pursue Doctoral Research In Biomedical Genomics, Including Statistical Genomics, At The National Institute Of Biomedical Genomics (Nibmg), Kalyan
Eligibility conditions for specific areas of research are :
Statistical Genomics : An applicant who wishes to pursue research in Statistical Genomics should hold a Master's degree (First class or equivalent) in a relevant discipline (Statistics, Mathematics, Bioinformatics, or a related discipline)
Biomedical Genomics : An applicant who wishes to pursue research in any area of biomedical genomics, other than statistical genomics, should hold a Master's degree (First class or equivalent) in a relevant discipline (Biochemistry, Biotechnology, Molecular Biology, Genetics, Zoology, Physiology, or a related discipline)
Fellowship : An applicant should have passed the NET conducted by CSIR/UGC/ICMR/DBT within the past ONE year AND should have been awarded a valid Junior Research Fellowship from CSIR, UGC, ICMR, DBT (Category-I only), DST (INSPIRE), NBHM. Preference will be given to candidates with demonstrable research training in the form of summer training or short-term courses in established research laboratories in preparation for a research career in biomedical sciences
How to apply
Online application will be accepted until 5 PM of December 31, 2015. A formal interview of the short-listed candidates will be held on January 12, 2016

More at http://www.nibmg.ac.in/?q=Career%20Opportunities

Katju Lab

Fri, 26 Feb 2016 03:25:32 -0600

TheLab seek to understand the genetic factors contributing to genomic variation and phenotypic diversity. To this end, we employ molecular and bioinformatic tools to study evolutionary processes at the level of populations, both experimental and natural, and genomes. Our research interests encompass a wide range of topics, including the evolution of organellar and nuclear genomes, gene duplication and the origin of novel function, and the fitness and phenotypic consequences of mutation in evolution. For details regards ongoing projects, please see the Research page.

http://katjulab.com/research.html

Research Scientist at IIT Madras

Mon, 07 Mar 2016 04:06:13 -0600

Research Scientist/Project Associate/Project Assistant Jobs opportunity in Indian Institute of Technology Madras (IIT Madras)

Research Scientist

Qualification : Ph.D in any branch of life science or bioinformatics or computational biology Experience : Previous experience in Molecular Biology, Cell Biology, Biochemistry and Genome/big data analysis is desirable but not mandatory

No. of Vacancy : 02

Project Associate

Qualification : MSc in any branch of life science Experience Previous experience in Molecular Biology, Cell Biology and Biochemistry is desirable but not mandatory

No. of Vacancy : 02

Project Assistant

Qualification : BSc in any branch of life science or chemical science Experience Previous experience any branch in Life science, Molecular Biology, Cell Biology and Biochemistry is desirable but not mandatory

No. of Vacancy : 03
How to apply

Interested candidates can forward their profiles to email id: nctb@iitm.ac.in latest by 18th March, 2016

More at https://www.iitm.ac.in/content/national-cancer-tissue-bio-bank-department-biotechnology-iitm-chennai-vacancy-various-post
https://www.iitm.ac.in/sites/default/files/notices/vacancy.pdf

Research Fellow Bioinformatics at Central University of Rajasthan

Tue, 02 Feb 2016 00:04:50 -0600

Research Fellow Bioinformatics

Eligibility : MSc(Bio-Chemistry, Bio-Informatics, Bio-Tech)
Location : Ajmer
Last Date : 13 Feb 2016
Hiring Process : Face to Face Interview
Central University of Rajasthan

Research Fellow Job vacancies in Central University of Rajasthan

Project Title : “Development of natural product derived febrifugine ananlogues as a novel therapeutics against visceral leishmaniasis”

No. of Post : 01

Qualification : Master of Biochemistry, Biotechnology, Bioinformatics and related biological sciences with minimum 55%, Age limit as per government rule.

Desirable Experience : Candidates with experience in cell culture, Chemoinformatics, and Parasitology will be preferred.

Fellowship : Rs. 25,000/- p.m. consolidated for NET qualified (14,000/- p.m. consolidated for Non-NET)
How to apply

The candidates may apply on a plain paper, along with their curriculum vitae (including name, date of birth, academic qualification starting from 10th class, summary of research experience, email id, phone number and passport size photograph) and email to vkprajapati@curaj.ac.in or post the hard copy to the Dr. Vijay Kumar Prajapati PI, DST-SERB Project (YSS/2015/000716), Department of Biochemistry, School of Life Sciences, Central University of Rajasthan, Bandarsindri, Dist- Ajmer, Rajasthan, 305 817 on or before 13th February 2016.

More at http://www.curaj.ac.in/Default.aspx?PageId=241

n50PlottingTools

Jit — Mon, 08 Feb 2016 15:39:04 -0600

Tools to create plots showing N-statistics for genome assemblies

More at https://github.com/dentearl/n50PlottingTools

Address of the bookmark: https://github.com/dentearl/n50PlottingTools

RA at Central University of Rajasthan

Tue, 09 Feb 2016 03:53:35 -0600

Research Fellow Bioinformatics

Eligibility : MSc(Bio-Chemistry, Bio-Informatics, Bio-Tech)

Location : Ajmer

Last Date : 13 Feb 2016

Hiring Process : Face to Face Interview
Central University of Rajasthan