<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/29635?offset=1440 https://bioinformaticsonline.com/bookmarks/view/38829/nquire-a-statistical-framework-for-ploidy-estimation-using-ngs-short-read-data Thu, 31 Jan 2019 05:12:19 -0600 https://bioinformaticsonline.com/bookmarks/view/38829/nquire-a-statistical-framework-for-ploidy-estimation-using-ngs-short-read-data <![CDATA[nQuire: A statistical framework for ploidy estimation using NGS short-read data]]> 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

]]> Jit https://bioinformaticsonline.com/opportunity/view/8108/jrf-institute-of-cytology-preventive-oncology Sat, 01 Feb 2014 13:47:29 -0600 <![CDATA[JRF @ Institute of Cytology & Preventive Oncology]]> Institute of Cytology & Preventive Oncology (ICPO) which was initially established as Cytology Research Centre ( CRC ) by the Indian Council of Medical Research (ICMR) in 1979, came into the existence in 1989 when CRC was elevated to the level of Institute. ICPO was instituted with the main aim of promoting research in the field of cancers that are most prevalent in India with an emphasis on their early detection and prevention.

Candidates having the below mentioned qualifications may appear for Walk in Interview at ICPO on 5th Feb 2014 between 10.00 AM and 12.00 PM under the NIF project entitled "Prediction of drug tragets of chemical constituents present within non-codified medicinal plants" under Dr Subhash M.Agarwal, Scientist C

Position : JRF
No of Post : One
Pay : Rs 12000/- + 30% HRA

Desired Profile : M.Sc in Bioinformatics with good academic record. Candidate with experience in database development and scripting would be preferred
Age Limit : Below 28 years
Period : 2 months

Interested candidates may send their applications with bio-data by email (smagarwal@gmail.com) or post addressed to Dr Subhash M Agarwal, Scientist C, Bioinformatics Division, Institute of Cytology and Preventive Oncology (ICPO) I-7, Sector 39, Noida-201301 so as to reach latest by 04.02.14

Deadline : 04.02.14

http://icmr.nic.in/icmrnews/icpo_jrf.pdf

]]> https://bioinformaticsonline.com/bookmarks/view/40546/clincnv-detection-of-copy-number-changes-in-germlinetriosomatic-contexts-in-ngs-data Thu, 16 Jan 2020 23:16:02 -0600 https://bioinformaticsonline.com/bookmarks/view/40546/clincnv-detection-of-copy-number-changes-in-germlinetriosomatic-contexts-in-ngs-data <![CDATA[ClinCNV: Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data]]> 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

]]> Neel https://bioinformaticsonline.com/researchlabs/view/8385/peng-lab Tue, 18 Feb 2014 13:53:46 -0600 <![CDATA[Peng Lab]]> Peng Lab at Janelia Farm Research Campus, Howard Hughes Medical Institute focuses on data mining for bioinformatics and computational molecular biology, particularly, bioimage data mining and informatics. These bioimages include cellular and molecular images and related medical images.

* Analysis of Gene Expression Pattern Images: high-performance image analysis and mining for different model organisms, such as fruitfly, C. elegans, and mouse;
* Feature/Model Learning: developing algorithms and software

Location :Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, Virginia, USA.

http://research.janelia.org/peng/

]]> https://bioinformaticsonline.com/bookmarks/view/41146/lofreq-a-sequence-quality-aware-ultra-sensitive-variant-caller-for-ngs-data Tue, 18 Feb 2020 03:24:22 -0600 https://bioinformaticsonline.com/bookmarks/view/41146/lofreq-a-sequence-quality-aware-ultra-sensitive-variant-caller-for-ngs-data <![CDATA[LoFreq*: A sequence-quality aware, ultra-sensitive variant caller for NGS data]]> 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/

]]> BioStar https://bioinformaticsonline.com/opportunity/view/8442/assistant-professor-king-saud-university-riyadh Fri, 21 Feb 2014 05:57:18 -0600 <![CDATA[Assistant Professor @ King Saud University Riyadh]]> Qualifications: Candidates must have a Ph.D. and a strong background in Molecular and Cellular Biology, protein expression, FACS, or computational biology, and ability to work collaboratively.

This position will have a significant focus on providing analytical support for next generation sequencing data analysis – Exome-sequencing, Targetted sequencing as well as high-throughput genotyping on Illumina platform.

Job location:

Genome Research Chair
King Saud University, Riyadh-11451
KSA

Interested candidate may forward their CV to grcksu@gmail.com

]]> https://bioinformaticsonline.com/bookmarks/view/42917/fings-filters-for-next-generation-sequencing Sat, 27 Feb 2021 01:18:35 -0600 https://bioinformaticsonline.com/bookmarks/view/42917/fings-filters-for-next-generation-sequencing <![CDATA[FiNGS: Filters for Next Generation Sequencing]]> 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

]]> Neel https://bioinformaticsonline.com/opportunity/view/8466/srf-position-in-computational-systems-biology-computational-biology-group-iiit-delhi Sun, 23 Feb 2014 20:56:08 -0600 <![CDATA[SRF position in Computational Systems Biology Computational biology Group, IIIT-Delhi]]> An opportunity to perform research in DST supported project that involves building of mathematical models to understand the functional relationship between circadian rhythms and memory formation under stressful condition. In this project, mathematical model of circadian rhythms based on gene regulatory mechanisms will be unified with the mathematical model of calcium signal transduction pathway to understand and predict the formation of fear memory under stressful conditions. The research scholar will spend full time on this project to build new models and expected to contribute significantly to prepare the results for publication and presentation, and to contribute to grant proposals.

Required Qualifications: Masters in physics/chemistry/mathematics (or) MTech in bioengineering, chemical (or) Masters in any traditional field of science with outstanding performance throughout the program. Candidate should have cleared GATE/UGC-CSIR examinations. Applicant should have done basic mathematics courses like calculus, differential equations, numerical analysis etc in their degree program and have obtained good grades in those courses. Knowledge of MATLAB and C or at least one traditional programming language is absolutely necessary. Strong inclination to understand biological concepts is a must for this research work as this project is about modeling biological systems.

Salary: A fixed salary of Rs 18000 PM including HRA will be paid.

Last date for application: This advertisement is open until suitable candidate is found for the project.

Preferred Qualifications: - Expertise in dynamical systems theory, bifurcation theory, numerical simulations, parameter estimation.

Independence and high motivation for carrying out interdisciplinary research. - Excellent communication skills and ability to work independently. - Good working habits.

Interested candidates should submit both curriculum vitae and statement of interest in PDF format to sriramk@iiitd.ac.in and should clearly mention in the subject "Application for SRF".

]]> https://bioinformaticsonline.com/pages/view/44672/libraries-or-management-tools-for-high-throughput-sequencing-data Fri, 04 Oct 2024 02:45:06 -0500 https://bioinformaticsonline.com/pages/view/44672/libraries-or-management-tools-for-high-throughput-sequencing-data <![CDATA[Libraries or management tools for high throughput sequencing data]]>
  • GATB Library. The Genome Analysis Toolbox with de-Bruijn graph. A large part of tools developed by the GenScale team are based on this library.
    These methods enable the analysis of data sets of any size on multi-core desktop computers, including very huge amount of reads data coming from any kind of organisms such as bacteria, plants, animals and even complex samples (e.g. metagenomes). Among them are (the full is available here: https://gatb.inria.fr/software/):
  • LRez: C++ Library and toolkit for the barcode-based management and indexation of linked-read datasets.

    • Variant calling and/or genotyping

    • DiscoSNP++ and discoSnpRAD: Reference-free small variant discovery (SNPs and indels)
    • MindTheGap: Detection and assembly of large insertion variants
    • TakeABreak: reference-free inversion discovery tool
    • SVJedi: Structural Variant genotyper with long read data
    • SVJedi-graph: Structural Variant genotyper with long read data using a variation graph

    Sequence assembly

    • MinYS: reference-guided genome assembly in metagenomics data
    • MTG-link: local assembly tool for linked-read data
    • Minia: De novo short read assembler
    • de-novo pipeline: de-novo assembly pipeline (error correction / contigs / scaffolding) for genomes and meta-genomes
    • Mapsembler2: Targeted assembly (not maintained)

    Managing k-mers & indexation

    • findere: simple strategy for speeding up queries and for reducing false positive calls from any Approximate Membership Query data structure.
      • fimpera extends findere adding the abundance information.
    • kmtricks: modular tool suite for counting kmers, and constructing Bloom filters or kmer matrices, for large collections of sequencing data.
    • kmindex is a tool for indexing and querying sequencing samples. It is built on top of kmtricks.
    • back to sequences: Find sequences (reads, unitigs, genes) related to a set of kmers in large datasets, in a matter of seconds.
    • Backpack Quotient Filter: k-mer indexing data structure with abundance
    • short read connector: Detect similar reads from potentially large read set
    • DSK: Count K-mer in sequences

    Pangenome graph manipulation

    • Pancat: Pangenome Comparison and Analysis Toolkit
    • GFAGraphs: a Python library to handle pangenome graph files in GFA format.

    Comparative metagenomics with k-mers

    Species and bacterial strains identification

    • ORI: software using long nanopore reads to identify bacteria present in a sample at the strain level
    • StrainFLAIR: STRAIN-level proFiLing using vArIation gRaph

    General-purpose sequencing data manipulation

    • GASSST: long read mapper
    • Leon: short read compressor (now included in GATB-core)
    • Bloocoo: short read corrector
    • BCALM: Construct compacted de Bruijn graphs (unitigs)

     Protein Structure

    • A_Purva: Contact Map Overlap solver
    • MD-Jeep: Distance Geometry solver
    • CSA: Comparative Structural Alignment

    Workflow

    • SLICEE: parallel execution of bioinformatics workflows

    Comparative Genomics

    • CASSIS: detection of rearrangement breakpoints
    • PLAST: intensive bank-to-bank sequence comparison
    • DRJBreakpointFinder: detection and precise localization of excision sites in proviral segments
    ]]>     LEGE     https://bioinformaticsonline.com/researchlabs/view/12868/landry-lab Thu, 17 Jul 2014 14:33:57 -0500 <![CDATA[Landry Lab]]> EVOLUTIONARY AND INTEGRATIVE CELL BIOLOGY

    Our research is at the crossroad between cell biology, ecological genomics, systems biology, molecular evolution and population genetics. We study the architecture and evolution of protein and signalling networks.

    More at http://landrylab.ibis.ulaval.ca/

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