BOL: Related items

Genomic Scientist at UDSC

Thu, 28 May 2015 19:14:23 -0500

Centre for Genetic Manipulation of Crop Plants

Department of Genetics

University of Delhi South Campus

NEW DELHI – 110 021

WALK-IN-INTERVIEW FOR THE TEMPORARY POSITIONS OF RESEACH SCIENTIT & LAB / FIELD ATTENDANT

1 Research Scientist (RS) – 3

DBT, Ph. D.

Experience on DNA Markers, plant genome mapping and bioinformatics

Salary: 60,000 (Consolidated) + 5% annual increment

Date and time: 25.06.2015 at 10:30 AM

These temporary positions have been sanctioned in a DBT funded project for the Phase II on ‘Centre of Excellence on genome mapping and molecular breeding of Brassicas.’

The applicants are requested to register their names on the day of interview in the First Floor, Biotech Centre, Centre for Genetic Manipulation of Crop Plants, Department of Genetics before the stipulated time for the interview. Only the registered eligible candidates will be interviewed on the day in the Committee Room.

Applicants are requested to bring all related documents, in original and a set of photocopy, for verification.

No TA/DA will be paid for attending the interview.

www.du.ac.in/du/index.php?mact=News,cntnt01,detail,0&cntnt01articleid=5492&cntnt01returnid=83

GRIDSS: the Genomic Rearrangement IDentification Software Suite

Rahul Nayak — Sun, 17 May 2020 10:27:44 -0500

GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements. GRIDSS includes a genome-wide break-end assembler, as well as a structural variation caller for Illumina sequencing data. GRIDSS calls variants based on alignment-guided positional de Bruijn graph genome-wide break-end assembly, split read, and read pair evidence.

Address of the bookmark: https://github.com/PapenfussLab/gridss

PeGAS: A Comprehensive Bioinformatic Solution for Pathogenic Bacterial Genomic Analysis

LEGE — Mon, 01 Sep 2025 01:18:10 -0500

This is PeGAS, a powerful bioinformatic tool designed for the seamless quality control, assembly, and annotation of Illumina paired-end reads specific to pathogenic bacteria. This tool integrates state-of-the-art open-source software to provide a streamlined and efficient workflow, ensuring accurate insights into the genomic makeup of pathogenic microbial strains.

Address of the bookmark: https://github.com/liviurotiul/PeGAS

SVfinder: Tool for detecting genomic rearrangement form DNA-seq data

Robert M Willioms — Thu, 14 Dec 2017 15:51:40 -0600

SVfinder provides genome-wide detection of structural variants from next generation paired-end sequencing reads.

Address of the bookmark: https://github.com/cauyrd/SVfinder

EuGI: a novel resource for studying genomic islands to facilitate horizontal gene transfer detection in eukaryotes

Surabhi Chaudhary — Sat, 12 May 2018 07:26:59 -0500

SWGIS v2.0 along with the EuGI database, which houses GIs identified in 66 different eukaryotic species, and the EuGI web-resource, provide the first comprehensive resource for studying HGT in eukaryotes.

https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4724-8

Address of the bookmark: https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-018-4724-8

AccessSyRI: finding genomic rearrangements and local sequence differences from whole-genome assemblies

Jit — Sat, 01 Feb 2020 13:38:49 -0600

AccessSyRI: finding genomic rearrangements andlocal sequence differences from whole-genome assemblies

SyRI, a pairwise whole-genome comparison tool for chromosome-level assemblies. SyRI starts by finding rearranged regions and then searches for differences in the sequences, which are distinguished for residing in syntenic or rearranged regions. This distinction is important as rearranged regions are inherited differently compared to syntenic regions.

https://genomebiology.biomedcentral.com/articles/10.1186/s13059-019-1911-0

Address of the bookmark: https://github.com/schneebergerlab/syri

ReConPlot: an R package for the visualization and interpretation of genomic rearrangements

LEGE — Thu, 14 Dec 2023 12:33:19 -0600

ReConPlot (REarrangement and COpy Number PLOT), an R package that provides functionalities for the joint visualization of SCNAs and SVs across one or multiple chromosomes. ReConPlot is based on the popular ggplot2 package, thus allowing customization of plots and the generation of publication-quality figures with minimal effort.

Address of the bookmark: https://academic.oup.com/bioinformatics/article/39/12/btad719/7460198?login=false

dna2bit: an ultra-fast and accurate genomic distance estimation software

Neel — Wed, 13 Aug 2025 19:56:21 -0500

dna2bit: an ultra-fast and accurate genomic distance estimation software

dna2bit is a software tool developed in C++11, leveraging the capabilities of OpenMP for parallel computing and the popcount technique for efficient bit manipulation.

Address of the bookmark: https://github.com/lijuzeng/dna2bit

Mercator: Multiple Whole-Genome Orthology Map Construction

Jit — Tue, 19 May 2020 16:46:22 -0500

Whole-genome homology maps attempt to identify the evolutionary relationships between and within multiple genomes. The term "syntenic" is often used to describe regions of multiple genomes that are believed to have evolved from the same region in an ancestral genome. However, it has been pointed out that this use of the term is incorrect (Passarge et al. 1999) and thus we will use the terms "homologous", "orthologous", and "paralogous" instead. Ideally, given K genomes, we would like to identify all orthologous genomic regions as well as paralogous regions within each genome and hypothetical ancestral genome. Maps listing these relationships are extremely valuable to researchers performing comparative analyses of genomic sequence. Here we present our initial work in the form a program called Mercator that constructs orthology maps between multiple whole genomes.

Address of the bookmark: https://www.biostat.wisc.edu/~cdewey/mercator/

Computer simulation of genetic mechanism !!

Jit — Sun, 13 Mar 2016 09:29:56 -0500

Computer simulation is the discipline of designing a model of an actual or theoretical physical/biological system, executing the model on a digital computer, and analyzing the execution output. Simulation embodies the principle of ``learning by doing'' --- to learn about the system we must first build a model of some sort and then operate the model. The use of simulation is an activity that is as natural as a child who role plays. Children understand the world around them by simulating (with toys and figurines) most of their interactions with other people, animals and objects. As adults, we lose some of this childlike behavior but recapture it later on through computer simulation. To understand reality and all of its complexity, we must build artificial objects and dynamically act out roles with them. Computer simulation is the electronic equivalent of this type of role playing and it serves to drive synthetic environments and virtual worlds. Within the overall task of simulation, there are three primary sub-fields: model design, model execution and model analysis

Simulation models have become important tools in Bioinformatics studies. There are many reasons for this, but we emphasize three of the more important:

(1) they enable exploration of hypotheses, and as such, have become invaluable means to guide research;

(2) they are unique approaches to integrate (in the literal term of the word) biological knowledge, in the form of experimental results; and

(3) they enable connecting biology with other fields of study ranging from physiology to genomics;

This blog, and this software list, is intended to guide the potential user of simulation models.
It is not, in any way, meant to be comprehensive on the very diverse simulation tools that already exist, but focuses on mechanistic, dynamic models. Similarly, it is not meant to provide any coverage of the breadth of applications; however, for interested readers, we provide references to use as a possible starting point.

Simulation models are meant to answer questions which scientists have in a dynamic, quantitative, and often, a pictorial way. Much of the bioinformatics research and its applications, in particular, involve a large number of components, actors, and factors. Assembling these in a coherent framework may seem a daunting task, especially for beginners, and can lead to confusion, even for experienced scientists, especially if the objectives of such an exercise are not well defined. Followings are the list of tools bioinformatician may use to analyze and provide answers to complex biological mechanisms and related problems.

Software Resource	Brief Description and Homepage
Aladyn	Tools to investigate how demographic parameters, populations genetics and abiotic conditions affect the rate of adaptation http://www.katja-schiffers.eu/research.html
ALF	A Simulation Framework for Genome Evolution http://www.cbrg.ethz.ch/alf
ART	ART is a set of simulation tools to generate synthetic next-generation sequencing data by mimicking real sequencing process with empirical error models or quality profiles. http://www.niehs.nih.gov/research/resources/software/biostatistics/art/
BAMSurgeon	Methods for realistic simulation of mutations in real data. https://github.com/adamewing/bamsurgeon
Bayesian Serial SimCoal	Bayesian Serial SimCoal, (BayeSSC) is a modification of SIMCOAL 1.0, a program written by Laurent Excoffier, John Novembre, and Stefan Schneider. http://www.stanford.edu/group/hadlylab/ssc/index.html
BaySICS	An integral platform with a graphical interface for statistical inference based on approximate Bayesian computation. https://sites.google.com/site/baysicsabc/
BEERS	BEERS was designed to benchmark RNA-Seq alignment algorithms and also algorithms that aim to reconstruct different isoforms and alternate splicing from RNA-Seq data http://cbil.upenn.edu/beers/
BOTTLENECK	Bottleneck is a program for detecting recent effective population size reductions from allele data frequencies http://www.ensam.inra.fr/urlb/bottleneck/bottleneck.html
BottleSim	BottleSim is a computer simulation program for simulating the process of population bottlenecks http://chkuo.name/software/bottlesim.html
CASS	Protein Sequence Simulation https://liberles.cst.temple.edu/software/cass/index.html
CDPOP	CDPOP is a landscape genetics tool for simulating the emergence of spatial genetic structure in populations resulting from specified landscape processes governing organism movement behavior. http://cel.dbs.umt.edu/cdpop
Classical Genetics Simulator	Web-based simulation software http://www.cgslab.com/
CoaSim	CoaSim is a tool for simulating the coalescent process with recombination and geneconversion under various demographic models. http://users-birc.au.dk/mailund/coasim/index.html
cosi	The cosi package is written in C and is available as a tar file. http://www.broadinstitute.org/~sfs/cosi/
CS-PSeq-Gen	A program to simulate the evolution of protein sequences under the constraints of the information of a particular reconstructed phylogeny http://bioserv.rpbs.univ-paris-diderot.fr/software/cs-pseq-gen/
DAWG	An application designed to simulate the evolution of recombinant DNA sequences in continuous time http://scit.us/projects/dawg
Easypop	EASYPOP is an individual based model intended to simulate datasets under a very broad range of conditions http://www.unil.ch/dee/en/home/menuinst/softwares--dataset/softwares/easypop.html
EggLib	EggLib is a C++/Python library and program package for evolutionary genetics and genomics. http://egglib.sourceforge.net/
EpiSIM	EpiSIM: simulation of multiple epistasis, linkage disequilibrium patterns and haplotype blocks for genome-wide interaction analysis https://sourceforge.net/projects/episimsimulator/files/
EvolSimulator	A simulation test bed for hypotheses of genome evolution http://acb.qfab.org/acb/evolsim/
EvolveAGene	A realistic coding sequence simulation program that separates mutation from selection and allows the user to set selection conditions http://bellinghamresearchinstitute.com/software/index.html
fastsimcoal	A continuous-‐time coalescent simulator of genomic diversity under arbitrarily complex evolutionary scenarios http://cmpg.unibe.ch/software/fastsimcoal/
FastSLINK	Simulation of Marker and Phenotype Data in Pedigrees https://watson.hgen.pitt.edu/
FFPopSim	C++/Python library for population genetics. http://webdav.tuebingen.mpg.de/ffpopsim/
FLUX SIMULATOR	The Flux Simulator aims at providing a deterministic in silico reproduction of the experimental pipelines for RNA-Seq, employing a minimal set of parameters. http://sammeth.net/confluence/display/sim/home
forqs	Forward-in-time simulation of Recombination, Quantitative Traits, and Selection https://bitbucket.org/dkessner/forqs
ForSim	ForSim: A Forward Evolutionary Computer Simulation http://anth.la.psu.edu/research/weiss-lab/research/research
ForwSim	The program given below is based on the algorithm described in Padhukasahasram et al. 2008 to simulate genetic drift in a standard Wright-Fisher process. http://badri-populationgeneticsimulators.blogspot.com/
FPG	Forward Population Genetic simulation https://bio.cst.temple.edu/~hey/software/software.htm#fpg
FREGENE	FREGENE is a C++ program that simulates sequence-like data over large genomic regions in large diploid populations. http://www.ebi.ac.uk/projects/bargen
FIGG	FIGG is a genome simulation tool that uses known or theorized variation frequency, per a given fragment size and grouped by GC content across a genome to model new genomes in FASTA format while tracking applied mutations for use in analysis http://insilicogenome.sourceforge.net/
fwdpp	A C++ template library for implementing efficient forward simulations. http://molpopgen.github.io/fwdpp/
GAMETES	Genetic Architecture Model Emulator for Testing and Evaluating Software: Simulates complex SNP models with pure, strict epistatic interactions with n-loci. http://sourceforge.net/projects/gametes/?source=navbar
GASP	Genometric Analysis Simulation Program. A software tool for testing and investigating methods in statistical genetics by generating samples of family data based on user specified models. http://research.nhgri.nih.gov/gasp/
GCTA	Genome-wide Complex Trait Analysis http://www.complextraitgenomics.com/software/gcta/download.html
GemSIM	Next generation sequencing read simulator http://sourceforge.net/projects/gemsim/
GeneArtisan	Simulation of Markers in Case-Control Study Designs http://www.rannala.org/?page_id=241
GENOME	A rapid coalescent-based whole genome simulator http://www.sph.umich.edu/csg/liang/genome/
GenomePop2	GenomePop2 is a specialization of the program GenomePop just to manage SNPs under more flexible and useful settings. If you need models with more than 2 alleles please use the GenomePop program version. https://ritchielab.psu.edu/research/research-areas/statistical-genetics-and-gen-epi/methods/genomesimla
GenomeSimla	GenomeSIMLA is currently under development- however, we have a beta release that we are asking to be tested http://chgr.mc.vanderbilt.edu/genomesimla/
GENS2	Simulates interactions among two genetic and one environmental factor and also allows for epistatic interactions. https://sourceforge.net/projects/gensim/
GWAsimulator	A rapid whole genome simulation program http://biostat.mc.vanderbilt.edu/wiki/main/gwasimulator
HAP-SAMPLE	An association simulator for candidate regions or genome scans http://www.hapsample.org/
HAPGEN	A simulator for the simulation of case control datasets at SNP markers https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html
HapSim	A simulation tool for generating haplotype data with pre-specified allele frequencies and LD coefficients http://cran.r-project.org/web/packages/hapsim/index.html
HAPSIMU	A program that simulates heterogeneous populations with various known and controllable structures under the continuous migration model or the discrete model http://l.web.umkc.edu/liujian/
IBDsim	IBDSim is a computer package for the simulation of genotypic data under general isolation by distance models. http://raphael.leblois.free.fr/
indel-Seq-Gen	A biological sequence simulation program that simulates highly divergent DNA sequences and protein superfamilies http://bioinfolab.unl.edu/~cstrope/isg/
Indelible	A powerful and flexible simulator of biological evolution http://abacus.gene.ucl.ac.uk/software/indelible/
invertFREGENE	InvertFREGENE is a forward-in-time simulator of inversions in population genetic data http://www.ebi.ac.uk/projects/bargen/
kernalPop	A spatially explicit population genetic simulation engine http://cran.r-project.org/src/contrib/archive/kernelpop/
MaCS	Markovian Coalescent Simulator http://www-hsc.usc.edu/~garykche/
Marlin	Marlin provides a user-friendly interface for performing forward-in-time population genetic simulations. http://www.patrickmeirmans.com/software/marlin.html
Mason	A package for the simulation of nucleotide data. http://www.seqan.de/projects/mason/
mbs	modifying Hudson's ms software to generate samples of DNA sequences with a biallelic site under selection http://www.sendou.soken.ac.jp/esb/innan/innanlab/software.html
Mendel's Accountant	Mendel's Accountant (MENDEL) is an advanced numerical simulation program for modeling genetic change over time and was developed collaboratively by Sanford, Baumgardner, Brewer, Gibson and ReMine http://mendelsaccount.sourceforge.net/
MetaPopGen	Simulates genetics in large size metapopulations https://sites.google.com/site/marcoandrello/metapopgen
MetaSim	A tool to generate collections of synthetic reads that reflect the diverse taxonomical composition of typical metagenome data sets http://ab.inf.uni-tuebingen.de/software/metasim/
mlcoalsim	Multilocus Coalescent Simulations http://code.google.com/p/mlcoalsim-v1/
ms	The purpose of this program is to allow one to investigate the statistical properties of such samples, to evaluate estimators or statistical tests, and generally to aid in the interpretation of polymorphism data sets. http://home.uchicago.edu/~rhudson1/source/mksamples.html
msHOT	The purpose of this program is to allow one to investigate the statistical properties of such samples, to evaluate estimators or statistical tests, and generally to aid in the interpretation of polymorphism data sets. http://home.uchicago.edu/~rhudson1/
msms	A coalescent Simlation tool with selection. http://www.mabs.at/ewing/msms/index.shtml
MySSP	A program for the simulation of DNA sequence evolution across a phylogenetic tree http://www.rosenberglab.net/software.html
Nemo	A forward-time, individual-based, genetically explicit, and stochastic simulation program designed to study the evolution of genetic markers, life history traits, and phenotypic traits in a flexible (meta-)population framework. http://nemo2.sourceforge.net/
NetRecodon	Coalescent simulation of coding DNA sequences with recombination (inter and intracodon), migration and demography http://code.google.com/p/netrecodon/
OncoSimulR	BioConductor package for Forward Genetic Simulation of Cancer Progresion with Epistasis https://github.com/rdiaz02/oncosimul
PEDAGOG	Software for simulating eco-evolutionary population dynamics https://bcrc.bio.umass.edu/pedigreesoftware/node/5
phenosim	A tool to add phenotypes to simulated genotypes http://evoplant.uni-hohenheim.de/doku.php?id=software:software
PhyloSim	An R package for the Monte Carlo simulation of sequence evolution http://www.ebi.ac.uk/goldman-srv/phylosim/
pIRS	Profile-based Illumina pair-end reads simulator https://code.google.com/p/pirs/
ProteinEvolver	Simulation of protein evolution along phylogenies under structure-based substitution models http://code.google.com/p/proteinevolver/
QMSim	QTL and Marker Simulator http://www.aps.uoguelph.ca/~msargol/qmsim/
quantiNEMO	An individual-based program for the analysis of quantitative traits with explicit genetic architecture potentially under selection in a structured population http://www2.unil.ch/popgen/softwares/quantinemo/
RECOAL	Simulates new haplotype data from a reference population of haplotypes. ftp://popgen.usc.edu/
Recodon	Coalescent simulation of coding DNA sequences with recombination, migration and demography http://code.google.com/p/recodon/
rlsim	A package for simulating RNA-seq library preparation with parameter estimation http://bit.ly/rlsim-git
Rmetasim	Rmetasim is a front-end for the metasim engine that is implemented as a package that runs in the statistical computing environment R http://cran.r-project.org/web/packages/rmetasim/index.html
RNA Seq Simulator	RSS takes SAM alignment files from RNA-Seq data and simulates over dispersed, multiple replica, differential, non-stranded RNA-Seq datasets. http://useq.sourceforge.net/cmdlnmenus.html#rnaseqsimulator
Rose	Random model of sequence evolution http://bibiserv.techfak.uni-bielefeld.de/rose/
scrm	A coalescent simulator optimized for long sequences and large samples. https://scrm.github.io/
SelSim	SelSim is a program for Monte Carlo simulation of DNA polymorphism data for a recom- bining region within which a single bi-allelic site has experienced natural selection http://www.well.ox.ac.uk/~spencer/selsim/
Seq-Gen	An application for the Monte Carlo simulation of molecular sequence evolution along phylogenetic trees. http://tree.bio.ed.ac.uk/software/seqgen/
SEQPower	Statistical power analysis for sequence-based association studies http://bioinformatics.org/spower/
SeqSIMLA	SeqSIMLA can simulate sequence data with user-specified disease and quantitative trait models. Family or unrelated case-control data can be simulated. http://seqsimla.sourceforge.net/
Serial NetEvolve	A flexible utility for generating serially-sampled sequences along a tree or recombinant network http://biorg.cis.fiu.edu/sne/
SFS_CODE	SFS_CODE can perform forward population genetic simulations under a general Wright-Fisher model with arbitrary migration, demographic, selective, and mutational effects. http://sfscode.sourceforge.net/sfs_code/index/index.html
SIBSIM	Quantitative phenotype simulation in extended pedigrees http://sourceforge.net/projects/sibsim/
SimAdapt	A spatially explicit, individual-based, forward-time, landscape-genetic simulation model combined with a landscape cellular automaton. https://www.openabm.org/model/3137
SIMCOAL2	A coalescent program for the simulation of complex recombination patterns over large genomic regions under various demographic models http://cmpg.unibe.ch/software/simcoal2/
SimCopy	An R package simulating the evolution of copy number profiles along a tree. http://bit.ly/simcopy
SIMLA	SIMLA is a SIMuLAtion program that generates data sets of families for use in Linkage and Association studies. http://dmpi.duke.edu/simla-simulation-software-version-32
SimPed	A Simulation Program to Generate Haplotype and Genotype Data for Pedigree Structures http://bioinformatics.org/simped/
Simprot	A program to simulate protein evolution by substitution, insertion and deletion http://www.uhnresearch.ca/labs/tillier/software.htm#3
SimRare	Rare variant simulation and analysis tool http://code.google.com/p/simrare/
simuGWAS	A forward-time simulator that simulates realistic samples for genome-wide association studies. http://simupop.sourceforge.net/cookbook/simugwas
simuPOP	simuPOP is a general-purpose individual-based forward-time population genetics simulation environment. http://simupop.sourceforge.net/
SISSI	A software tool to generate data of related sequences along a given phylogeny, taking into account user defined system of neighbourhoods and instantaneous rate matrices. http://www.cibiv.at/software/sissi/
SMARTPOP	Simulating Mating Alliance as a Reproductive Tactic for Populations http://smartpop.sourceforge.net/
SNPsim	Coalescent simulation of hotspot recombination http://code.google.com/p/phylosoftware/
SPIP	SPIP simulates the transmission of genes from parents to offspring in a population having demographic structure defined by the user http://swfsc.noaa.gov/textblock.aspx?division=fed&id=3434
Splatche	Spatial and Temporal Coalescences in Heterogeneous Environment http://www.splatche.com/
srv	Simulator of Rare Varaints (srv) is a simulator for the simulation of the introduction and evolution of (rare) genetic variants. http://simupop.sourceforge.net/cookbook/simurarevariants
SUP	SLINK/FastSLINK utility program http://mlemire.freeshell.org/software.html
TreesimJ	A flexible, forward-time population genetic simulator http://code.google.com/p/treesimj/
Variant Simulation Tools	A simulation tool for post-GWAS genetic epidemiological studies using whole-genome or whole-exome next-gen sequencing data, with an emphasis on user-friendliness and reproducibility. http://varianttools.sourceforge.net/simulation/homepage
Vortex	VORTEX is an individual-based simulation model for population viability analysis (PVA). http://www.vortex9.org/vortex.html
Wessim	Whole Exome Sequencing SIMulator http://sak042.github.io/wessim/