BOL: Related items

AMStat: display statistics of large sequence files from next generation sequencing projects

Neel — Fri, 09 Nov 2018 13:34:56 -0600

SAMStat is an efficient C program to quickly display statistics of large sequence files from next generation sequencing projects. When applied to SAM/BAM files all statistics are reported for unmapped, poorly and accurately mapped reads separately. This allows for identification of a variety of problems, such as remaining linker and adaptor sequences, causing poor mapping. Apart from this SAMStat can be used to verify individual processing steps in large analysis pipelines.

Address of the bookmark: http://samstat.sourceforge.net/

Research Fellow @ Mendel laboratory

Tue, 26 Nov 2013 00:07:57 -0600

IRCCS Casa Sollievo della Sofferenza – Mendel laboratory is seeking one talented bioinformatician (Rome)
Start date: immediate

Duration: 1 year

Funding Source: Institutional
Salary on grant: B2 (€ 22.000/year gross)
Contact Person (Referent): Tommaso Mazza
Ref. E-Mail: t.mazza@css-mendel.it
Tel: +39 06 44160526
Fax: +39 06 44160548

Job Description: The bioinformatics unit at IRCCS Casa Sollievo della Sofferenza - Mendel laboratory in Rome is looking for one young PhD bioinformatician with specific experience and/or interest in the analysis of transcriptomic data.

The candidate will be mainly in charge of developing research on a range of hot applications and projects, dealing with microarrays, RNA-Seq and miRNA-Seq data. Main activities will be: (i) data analysis (short-reads mapping, variants call and annotation, functional enrichment analysis of gene expression data); (ii) networks analysis and simulation (artificial knockout, redundancy and lethality analysis, gene set essentiality); (iii) developing of ad-hoc software solutions/routines on clusters of CPUs and GPUs.

The correct cultural background (training in Biology / Computer Science / Statistics or a mix of the three) and a strong interest in working with high throughput data analysis will be considered at the same level of specific experience in the above-mentioned fields.
Knowledge of molecular modeling and simulation and one of these languages: python, perl, R, Java, C++, C# is a golden plus. Good knowledge of Scientific English will be positively evaluated for this position, together with good presentation and teamwork skills.

A CV with one professional reference, details on educational background and of the biological and/or bioinformatic and/or data analysis skills and experience should be sent by email for a preliminary selection to: Tommaso Mazza, CSS-Mendel: t.mazza@css-mendel.it

Context
Casa Sollievo della Sofferenza is an Institute for hospitalization, care, and scientific research located in San Giovanni Rotondo, Italy. It integrates clinical assistance (with inpatient and outpatient facilities) and research. It has an affiliate institute, CSS-Mendel, located in Rome. Between the two sites, it employs over 100 researchers who focus on genetics. The Center is equipped with state of the art genomics technology (SOLiD 5500XL next generation sequencer, Illumina MiSeq, Affymetrix/Agilent microarray platforms, etc) as well as a dedicated high performance computing facility, a non-conventional workstation of GPUs and a short- and long-term storage disk.

Applications
Candidates should send:
• a cover letter explaining the role they would like to undertake within the Center, even if it is not listed in this job adv, stating clearly why they would be a good fit to the proposed role, and what they would bring to the Center in terms of expertise, ideas, talent;
• a CV including a list of publications;
• List of referees;

More at http://www.css-mendel.it/

nQuire: A statistical framework for ploidy estimation using NGS short-read data

Jit — Thu, 31 Jan 2019 05:12:19 -0600

nQuire implements a set of commands to estimate ploidy level of individuals from species, where recent polyploidization occurred and intraspecific ploidy variation is observed. Specifically, nQuire uses next-generation sequencing data to distinguish between diploids, triploids and tetraploids, on the basis of frequency distributions at variant sites where only two bases are segregating.

For more background see also the publication at BMC Bioinformatics.

https://github.com/clwgg/nQuire

Address of the bookmark: https://github.com/clwgg/nQuire

Bioinformatics group at Boku University

Thu, 12 Dec 2013 17:53:10 -0600

The Bioinformatics group at Boku University has two main areas of interest, underpinning a common goal, the study of complex systems in living organisms. To overcome the engineered redundancies and combinatorial effects prevalent in higher eukaryotes, novel views augmenting the classical gene by gene approaches are required. We combine

1. Work to establish improved quantitative experimental assays (such as microarrays or differential in-gel electrophoresis) and
2. Development of modern computational methods (such as hierarchical probabilistic models or integration of heterogeneous data sources)

Lab page @ http://bioinf.boku.ac.at/

ClinCNV: Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data

Neel — Thu, 16 Jan 2020 23:16:02 -0600

ClinCNV detects CNVs in germline and somatic context in NGS data (targeted and whole-genome). We work in cohorts, so it makes sense to try ClinCNV if you have more than 10 samples (recommended amount - 40 since we estimate variances from the data). By "cohort" we mean samples sequenced with the same enrichment kit with approximately the same depth (ie 1x WGS and 30x WGS better be analysed in separate runs of ClinCNV). Of course it is better if your samples were sequenced within the same sequencing facility.

Address of the bookmark: https://github.com/imgag/ClinCNV

Free math books

Manisha Mishra — Thu, 12 Dec 2013 19:38:34 -0600

Bioinformatics require some match skills, therefore I decided to provide this wonderful math eBooks links to the BOL community.

Please add ur links/bookmarks in comment section.

Address of the bookmark: http://physicsdatabase.com/free-math-books/

LoFreq*: A sequence-quality aware, ultra-sensitive variant caller for NGS data

BioStar — Tue, 18 Feb 2020 03:24:22 -0600

LoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or base/indel alignment uncertainty), which are usually ignored by other methods or only used for filtering.

https://github.com/CSB5/lofreq

http://csb5.github.io/lofreq/installation/

https://github.com/CSB5/lofreq/tree/master/dist

Address of the bookmark: http://csb5.github.io/lofreq/

Bioinformatics software for biologists in the genomics era

Poonam Mahapatra — Sun, 22 Dec 2013 17:31:05 -0600

The genome sequencing revolution is approaching a landmark figure of 1000 completely sequenced genomes. Coupled with fast-declining, per-base sequencing costs, this influx of DNA sequence data has encouraged laboratory scientists to engage large datasets in comparative sequence analyses for making evolutionary, functional and translational inferences. However, the majority of the scientists at the forefront of experimental research are not bioinformaticians, so a gap exists between the user-friendly software needed and the scripting/programming infrastructure often employed for the analysis of large numbers of genes, long genomic segments and groups of sequences. We see an urgent need for the expansion of the fundamental paradigms under which biologist-friendly software tools are designed and developed to fulfill the needs of biologists to analyze large datasets by using sophisticated computational methods. We argue that the design principles need to be sensitive to the reality that comparatively small teams of biologists have historically developed some of the most popular biological software packages in molecular evolutionary analysis. Furthermore, biological intuitiveness and investigator empowerment need to take precedence over the current supposition that biologists should re-tool and become programmers when analyzing genome scale datasets.

Address of the bookmark: http://bioinformatics.oxfordjournals.org/content/23/14/1713.full

FiNGS: Filters for Next Generation Sequencing

Neel — Sat, 27 Feb 2021 01:18:35 -0600

Key features

Filters SNVs from any variant caller to remove false positives
Calculates metrics based on BAM files and provides filtering not possible with other tools
Fully user-configurable filtering (including which filters to use and their thresholds)
Option to use filters identical to ICGC recommendations

FiNGS provides researchers with a tool to reproducibly filter somatic variants that is simple to both deploy and use, with filters and thresholds that are fully configurable by the user. It ingests and emits standard variant call format (VCF) files and will slot into existing sequencing pipelines. It allows users to develop and implement their own filtering strategies and simple sharing of these with others.

FiNGS reliably improves upon the precision of default variant caller outputs and performs better than other tools designed for the same task.

Address of the bookmark: https://github.com/cpwardell/FiNGS

JRF @ PONDICHERRY UNIVERSITY

Fri, 03 Jan 2014 16:48:56 -0600

PONDICHERRY UNIVERSITY

CENTRE FOR BIOINFORMATICS

PUDUCHERRY

Applications are invited for one Project Assistant to work in the UGC sponsored Research Award "Molecular Docking and Dynamics studies to understand the interacting mechanism of oncogenic 101 protein with its cellular proteins".

The duration for the fellowship is 12months only with consolidated pay ofRs. 5,000 per month.

Application on plain paper with following details: Name, Address, Data of Birth, Father's Name, Nationality, Educational Qualification (SSLC onwards-enclose attested copies of certificate) and Researcb Experience may be addressed to Dr. R. Krishna, Principle Investigator (PI), UGC Research Award, Centre for Bioinformatics, Pondicherry University, Pondicherry - 605 014.

Application should reach in January 261h , 2013.

Essential Qualification: M.Sc. in Bioinformatics/Biophysics with good academic record.

Qualification for Project Fellow:

M.Sc in Bioinformatics/Biophysics.

The person to be considered for appointment as Project Fellow must have second class master degree with a minimum of 55% marks in the subject concerned or a related subject.

The candidate to be appointed as Project Fellows should be below thc age of40 years at the time of appointment.

Desirable Qualification for this Project: Research Experience in Small/Macromolecule Crystallography and Structural Bioinformatics.

For more details, refer the web site: www.pondiuni.edu.in/sites/default/files/BIC-311213.pdf