BOL: Related items

Kmer: a suite of tools for DNA sequence analysis

BioStar — Wed, 18 Aug 2021 00:02:54 -0500

More at https://help.rc.ufl.edu/doc/Kmer

This also includes:

A2Amapper: ATAC, Assembly to Assembly Comparision tool:
- Comparative mapping between two genome assemblies (same species), or between two different genomes (cross species).

Sim4db:
- Spliced alignment of cDNA and genomic sequences, from the same (sim4) or related (sim4cc) species. Optimized for high-throughput batched alignment.

LEAFF:
- LEAFF (ahem, Let's Extract Anything From Fasta) is a utility program for working with multi-fasta files. In addition to providing random access to the base level, it includes several analysis functions.

Meryl:
- An out-of-core k-mer counter. The amount of sequence that can be processed for any size k depends only on the amount of free disk space.

Address of the bookmark: https://help.rc.ufl.edu/doc/Kmer

PRISM

Jit — Sat, 10 Dec 2016 15:19:40 -0600

PRISM is a software for split read (reads which span across a structrual variant -- SV ) mapping and SV calling from the mapping result. PRISM is able to detect small insertions and abitrary size deletions, inversions and tandom duplications with the direction of discordant read pairs. PRISM_CTX is a tool for detecting inter-chromosome trans-location events.

PRISM and PRISM_CTX were originally designed and written by Michael Brudno and Yue Jiang, The original PRISM publication can be found here.

The authors may be contacted via e-mail at: prism at cs.toronto.edu.

Additional information is available in the PRISM README file and PRISM_CTX README file.

http://compbio.cs.toronto.edu/prism/

Address of the bookmark: http://compbio.cs.toronto.edu/prism/

InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams

Jit — Wed, 29 Jun 2022 03:22:26 -0500

InteractiVenn, a more flexible tool for interacting with Venn diagrams including up to six sets. It offers a clean interface for Venn diagram construction and enables analysis of set unions while preserving the shape of the diagram. Set unions are useful to reveal differences and similarities among sets and may be guided in our tool by a tree or by a list of set unions. The tool also allows obtaining subsets’ elements, saving and loading sets for further analyses, and exporting the diagram in vector and image formats. InteractiVenn has been used to analyze two biological datasets, but it may serve set analysis in a broad range of domains.

More at https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-015-0611-3

Address of the bookmark: http://www.interactivenn.net/

Postdoc at UBritishColumbia in TroutGenomics

Thu, 22 Dec 2016 08:18:46 -0600

Landscape Genomics Postdoc at UBC A research team at the University of British Columbia’s Department of Zoology and Biodiversity Research Centre is seeking a postdoctoral researcher in landscape genetics of native rainbow trout (Oncorhynchus mykiss).

This project is part of a larger Genome Canada project on genetics and physiology of adaptation to climate change in rainbow trout, and the population genomics component is in the labs of Eric Taylor and Michael Whitlock. The landscape genomics component primarily involves whole genome sequencing approaches to understanding the genomic basis of adaptation to features of habitat, but also to provide insights into phylogeography and the influence of watershed structure on population subdivision in rainbow trout. A PhD in a related field with expertise in basic theory and bioinformatic analysis of population genomics data is required.

The position is available for one year with renewal for up to three additional years. Salary is $55,000 per year plus benefits. To apply, please send a brief cover letter summarizing your qualifications for the position, a CV, and the names, addresses, phone numbers and emails of three references.

Review of applications will begin January 16, 2017. Address application materials to etaylor@zoology.ubc.ca to whom any questions can also be addressed. etaylor@zoology.ubc.ca

Omega2: metagenome assembly pipeline

Jit — Mon, 10 Jul 2017 05:56:07 -0500

Omega found overlaps between reads using a prefix/suffix hash table. The overlap graph of reads was simplified by removing transitive edges and trimming short branches. Unitigs were generated based on minimum cost flow analysis of the overlap graph and then merged to contigs and scaffolds using mate-pair information. In comparison with three de Bruijn graph assemblers (SOAPdenovo, IDBA-UD and MetaVelvet), Omega provided comparable overall performance on a HiSeq 100-bp dataset and superior performance on a MiSeq 300-bp dataset. In comparison with Celera on the MiSeq dataset, Omega provided more continuous assemblies overall using a fraction of the computing time of existing overlap-layout-consensus assemblers. This indicates Omega can more efficiently assemble longer Illumina reads, and at deeper coverage, for metagenomic datasets.

Address of the bookmark: http://omega.omicsbio.org/

Studentship

Tue, 24 Jan 2017 04:26:14 -0600

Advt. No. ACBR/BTBI/BIF/Manpower/ADV/16-17
Research Associate/ Studentship/ Traineeship Jobs opportunity in University of Delhi - Dr. B.R. Ambedkar Center for Biomedical Research (ACBR) on temporary basis
Studentship
No. of Post : 01
Qualifications : Applicants who are pursuing Post Graduate Degree course/ Diploma in Bioinformatics/ Biomedical Sciences/ Biotechnology/Life Sciences/Chemistry/ Biochemistry with a programme in Bioinformatics to carry out the project.
Remuneration : Rs. 8,000/-
Traineeship
No. of Post : 01
Qualifications : Applicants who have completed their Post Graduate degree in Bioinformatics /Biomedical Sciences/Biotechnology/Life Sciences/Chemistry/Biochemistry or any other branch of Life Sciences with knowledge in Bioinformatics
Remuneration : Rs. 8,000/-
Research Associate
No. of Post : 01
Qualifications : Ph.D. in Bio-Medical Sciences/Bioinformatics/ Biotechnology/Life Sciences/ Chemistry/ Bio-Chemistry and related areas
Remuneration : Rs. 36,000/-

Applicant are required to bring applications on plain paper, stating the name, address, date of birth. educational qualifications and experiences and Institute, along with attested photocopies of mark sheets and certificates etc. at the time of Interview. Applications should also be sent by Entail to Dr. Madhu Chopra, Coordinator, BIF Facility. Email: acbrdu.blisnet@nic.in; mchopradu@gmail.com.
Interview Date : 13.02.2017
Time : 10:00 am-12:00 noon
Venue : ACBR

Many-Core Engine (MCE) for Perl example

Jit — Tue, 31 Jan 2017 05:37:50 -0600

MCE spawns a pool of workers and therefore does not fork a new process per each element of data. Instead, MCE follows a bank queuing model. Imagine the line being the data and bank-tellers the parallel workers. MCE enhances that model by adding the ability to chunk the next n elements from the input stream to the next available worker.

CORE MODULES

Three modules make up the core engine for MCE.

MCE::Core: Provides the Core API for Many-Core Engine. The various MCE options are described here.
MCE::Signal: Temporary directory creation, cleanup, and signal handling.
MCE::Util: Utility functions for Many-Core Engine.

MCE EXTRAS

There are 4 add-on modules for use with MCE.

MCE::Candy: Provides a collection of sugar methods and output iterators for preserving output order.
MCE::Mutex: Provides a simple semaphore implementation supporting threads and processes.
MCE::Queue: Provides a hybrid queuing implementation for MCE supporting normal queues and priority queues from a single module. MCE::Queue exchanges data via the core engine to enable queuing to work for both children (spawned from fork) and threads.
MCE::Relay: Enables workers to receive and pass on information orderly with zero involvement by the manager process while running.

MCE MODELS

The models take Many-Core Engine to a new level for ease of use. Two options (chunk_size and max_workers) are configured automatically as well as spawning and shutdown.

MCE::Loop: Provides a parallel loop utilizing MCE for building creative loops.
MCE::Flow: A parallel flow model for building creative applications. This makes use of user_tasks in MCE. The author has full control when utilizing this model. MCE::Flow is similar to MCE::Loop, but allows for multiple code blocks to run in parallel with a slight change to syntax.
MCE::Grep: Provides a parallel grep implementation similar to the native grep function.
MCE::Map: Provides a parallel map model similar to the native map function.
MCE::Step: Provides a parallel step implementation utilizing MCE::Queue between user tasks. MCE::Step is a spin off from MCE::Flow with a touch of MCE::Stream. This model, introduced in 1.506, allows one to pass data from one sub-task into the next transparently.
MCE::Stream: Provides an efficient parallel implementation for chaining multiple maps and greps together through user_tasks and MCE::Queue. Like with MCE::Flow, MCE::Stream can run multiple code blocks in parallel with a slight change to syntax from MCE::Map and MCE::Grep.

MISCELLANEOUS

Miscellaneous additions included with the distribution.

MCE::Examples: Describes various demonstrations for MCE including a Monte Carlo simulation.
MCE::Subs: Exports functions mapped directly to MCE methods; e.g. mce_wid. The module allows 3 options; :manager, :worker, and :getter.

REQUIREMENTS

Perl 5.8.0 or later. PDL::IO::Storable is required in scripts running PDL.

SOURCE AND FURTHER READING

The source, cookbook, and examples are hosted at GitHub.

RGFA: powerful and convenient handling of assembly graphs

Rahul Nayak — Thu, 25 Jan 2018 05:47:53 -0600

RGFA, an implementation of the proposed GFA specification in Ruby. It allows the user to conveniently parse, edit and write GFA files. Complex operations such as the separation of the implicit instances of repeats and the merging of linear paths can be performed. A typical application of RGFA is the editing of a graph, to finish the assembly of a sequence, using information not available to the assembler. We illustrate a use case, in which the assembly of a repetitive metagenomic fosmid insert was completed using a script based on RGFA.

https://github.com/ggonnella/rgfa

Address of the bookmark: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5103826/

Open Positions in Pasini’s lab

Sat, 04 Feb 2017 08:17:18 -0600

Computational Biologists
Open to PhD-student and Post-doc candidates
We are looking for wet and computational biologists to work on an ERC funded project in our
laboratory located at the Department of Experimental Oncology of the European Institute of
Oncology in Milan (Italy). The project will focus on different aspects of the function of Polycomb
Group proteins and other chromatin modifying activities in relation to their role in regulating cellular
identity in the development of adult tissues.
The candidates will be in charge of computational analysis and data management related to the
project. She/he will directly interact with the wet scientists working in our laboratory while working
embedded in the community of computational biologists present at our institution. The work will
involve the analysis of sequencing data produced with cutting edge technologies to study gene
expression and chromatin environment including data produced on rare cell populations and single
cells. The applicants must have a good knowledge of programming in python/perl/java along with
strong statistical background and performing analysis in R platform. A biological background is
also recommended however it’s not mandatory for application.
Each applicant should submit a full CV (with a detailed description of her/his background,
expertise, achievements and publication records) together with a letter of intent and at least two
contacts for recommendations (for a post-doc position). Competitive salary will be offered based
on the experience of the candidate. Non Italian as well as Italian applicants that have been working
outside Italy (>3yrs.) will have the opportunity to benefit of a full tax deduction for the first three
years of contract.
Applications should be submitted as single PDF to diego.pasini@ieo.it

Lab https://www.ieo.it/en/RESEARCH/People/Researchers/Pasini-Diego/

fineSTRUCTURE v2 & GLOBETROTTER

Shruti Paniwala — Mon, 13 Feb 2017 08:40:23 -0600

Software available at this site

FineSTRUCTURE version 2, a pipeline for running ChromoPainter and FineSTRUCTURE for population inference. A GUI is available for interpretation. Download from the Downloads page.
FineSTRUCTURE R scripts, a facility for exploring the results when the GUI is unavailable.
GLOBETROTTER, the admixture dating method based on ChromoPainter. Download from the Downloads page.
AdmixturePainting, A set of R tools to inmterpret the results of ADMIXTURE and STRUCTURE-like mixture models.
RADpainter, finestructure and ChromoPainter for RAD tag data used for non-model organisms.
Scripts to perform many types of conversion. Included in the main software download from the Downloads page.

What this page is This page provides information about and downloads for methodology for Chromosome Painting. It is not a facility to analyse your genome. Sorry if you were misled by the punchy name!
About Chromosome Painting Painting is an efficient way of identifying important haplotype information from dense genotype data. It describes ancestry in an efficient way suitable for a range of further analyses, including population identification and admixture dating.

Address of the bookmark: http://paintmychromosomes.com/