BOL: Related items

Libraries or management tools for high throughput sequencing data

LEGE — Fri, 04 Oct 2024 02:45:06 -0500

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

Simka and SimkaMin: Comparative metagenomics for large-scale datasets
Comparead & Commet: comparison of metagenomic datasets

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

The Centre for Bioinformatics (MCB) Lab

Sun, 14 Jul 2013 12:41:20 -0500

The Centre for Bioinformatics (MCB) is a diverse collection of professors, postdoctoral fellows, and students, who share a common interest in Bioinformatics.

Research Area

We are interested in the development of the statistics and computational methods for the analysis of this data in breast cancer.
We have worked on probabilistic models for subcellular localization, protein-protein interactions, and problems related to chemical genomics.
We are interested in the development of bioinformatics/biostatistical methodology in the analysis of epigenetic/epigenomic data.
We are interested in integrative bioinformatics approaches to learn the gene, gene products, interactions, and regulatory mechanisms involved in mental retardation.

Link @ http://www.mcgill.ca/mcb/

The Ontario Institute for Cancer Research (OICR) Genomics Lab , Toronto, Canada.

Mon, 12 Aug 2013 01:43:13 -0500

The Human Genome Project led to the development of a wide array of technologies to screen the genome and its products (genes, proteins, metabolites) and molecules that interact with these products (chemicals, RNAi). The existence of these tools resulted in the creation of facilities that use robotics and informatics to generate high-throughput screens of DNA, RNA, protein, tissue, chemicals and other substances.

The genomics platform uses cancer genome sequencing and other high-throughput techniques to identify genes critical to the development of cancer and anomalies in the genomic profile of the tumours.

For more info visit : http://oicr.on.ca/

Pandey Lab

Fri, 20 Sep 2013 13:19:18 -0500

The Pandey Lab at Johns Hopkins University is a Systems Biology lab that combines molecular biology, analytical chemistry and computational biology with various "Omics" technologies including genomics and proteomics to understand signaling pathways and to identify therapeutic targets and biomarkers in a number of cancers.

More at http://pandeylab.igm.jhmi.edu/

http://scholar.google.com/citations?user=OhuG0FcAAAAJ&hl=en

Vvek's Lab

Thu, 26 Sep 2013 11:11:39 -0500

Broad Area of Research: RNA biology (microRNA, lncRNA), Stem cells, Functional genomics, Epigenomics and Cancer

RNAs, especially non-coding RNAs (such as microRNA, long ncRNAs) are recently identified to be very abundant in mammalian organisms and play some key roles in gene expression regulation, gene silencing, and also implicated in disease progression, stem cell pluripotency etc. Current research activities of our lab include analysis of expression pattern of ncRNAs by microarray and next-gen sequencing data and understanding the role of miRNAs or other regulatory RNAs in various diseases, especially cancer and validation by reporter assays (renilla/luciferase) and other experimental tools.

More @ http://vvekslab.in/index.html

University of California, Irvine - Center for Complex Biological Systems

Mon, 04 Nov 2013 17:10:29 -0600

The University of California Irvine's Center for Complex Biological Systems got its start just as there was a revolution in biology. Systems Biology requires that scientists work across many disciplines including engineering, physics and mathematics. The Center specializes in helping form the kinds of teams that will propel biological research into the future. It is also proud to be able to train students in the new interdisciplinary approach. http://ccbs.uci.edu

MATHomics Lab

Tue, 19 Nov 2013 18:17:32 -0600

Mathomics is a collaborative research group of the Center for Mathematical Modeling and the Center for Genome Regulation at University of Chile, created to play a central role in the development of biotechnological projects, providing state of the art bioinformatics and mathematical modeling tools, allowing to face these problems from the point of view of Systems Biology.

Lab page @ http://www.mathomics.cl/

Nieduszynski Group

Fri, 26 Sep 2014 19:35:06 -0500

Complete, accurate replication of the genome is essential for life. All chromosomes in eukaryotic cells must be duplicated and then segregated to daughter cells to ensure genetic integrity and produce the large number of cells that make up a multicellular organism. We are using genetic, genomic and computational methods to understand how chromosome replication is regulated to ensure genome stability. By focusing on the basic biology that underpins cell growth and division we aim to provide new insights that may help our understanding of diseases such as cancer and congenital disorders.

More http://www.nieduszynski.org/index.php
http://www.path.ox.ac.uk/research/cell-biology-and-pathology/conrad-nieduszynski-group

BUSCO

Jitendra Narayan — Sun, 07 Feb 2016 16:02:39 -0600

Assessing genome assembly and annotation completeness with Benchmarking Universal Single-Copy Orthologs

More at http://busco.ezlab.org/

Address of the bookmark: http://busco.ezlab.org/

Bioinformatician - Purdue Cancer Center

Wed, 03 Feb 2021 22:54:14 -0600

The Center for Cancer Research is an NCI-designated cancer center. The center is a catalyst for collaborative cancer research around Purdue University. In this role, the selected individual will have the opportunity to cooperate with Purdue faculty and students in performing cutting-edge research and analyses, with opportunities for professional development, and the possibility of co-authorship in faculty research publications.
Projects will be challenging, including various model organisms, and we are looking for an individual who is excited about interacting with multi-disciplinary cancer research groups and the development of new tools, techniques, and workflows. Independently perform both routine and project-specific analyses, advise faculty on the design of experiments, writing manuscripts for publication, and writing grant proposals. Interact and collaborate with bioinformatics services (i.e. Statistical Consulting Center to provide relevant services to the campus research community), where applicable. Support all of the bioinformatics activities of the Center for Cancer Research at Purdue University
Required:

Master's degree in bioinformatics, computer science, molecular biology, or related field
One year of experience in analyzing RNA-Seq data
In lieu of a degree, consideration will be given to an equivalent combination of related education and required work experience.
Understanding of molecular biology, biochemistry, and genetics
Proficiency in writing scripts using Perl, Python, Java, or equivalent languages
Proficiency in R and UNIX/LINUX
Knowledge of genomics, alignment, annotation, bioinformatics, concepts of sequence assembly
Highly motivated and detail-oriented
Ability, interest, and curiosity to learn new skills
Must possess strong communication skills to work effectively with users across disciplines
Ability to work independently and as part of a multi-disciplinary team
Strong visual, verbal, and written communication skills
Excellent time organizational skills
Preferred:

Experience writing software or building software pipelines
Experience with oncology-specific public databases including TCGA
Experience with deploying and/or running software on high-performance computational systems
Statistical and experimental design knowledge
Additional Information:

This position is contingent on the availability of funding
Purdue will not sponsor employment authorization for this position
A background check will be required for employment in this position
FLSA: Exempt (Not Eligible For Overtime)
Retirement Eligibility: Defined Contribution Waiting Period
Purdue University is an EOE/AA employer. All individuals, including minorities, women, individuals with disabilities, and veterans are encouraged to apply

More at https://careers.purdue.edu/job/West-Lafayette-Bioinformatician-Purdue-Cancer-Center-IN-47906/686617600/