CPAT - https://github.com/liguowang/cpat, http://lilab.research.bcm.edu/ (web server)

CPC2 - https://github.com/gao-lab/CPC2_standalone, http://cpc2.gao-lab.org/ (web server)

Infernal - http://eddylab.org/infernal/, https://github.com/EddyRivasLab/infernal

NCBI RefSeq - https://www.ncbi.nlm.nih.gov/refseq/

Rfam - http://rfam.xfam.org/, https://docs.rfam.org/en/latest/index.html

SILVA - https://www.arb-silva.de/

RNAmmer - http://www.cbs.dtu.dk/services/RNAmmer/ (web server, standalone download link)

Applications are invited for the post of Junior Research Fellow (JRF) in a DBT funded IYBA project entitled “Generatingaprotein-ncRNA interactome for Dorsal mediated gene regulation and dorso-ventral patterning genes in Drosophila” in the Lab. Of Molecular Biology at the Faculty of Life Sciences and Biotechnology, South Asian University, New Delhi. The project requires extensive use of molecular, genetic and genomic approaches.

POST: Junior Research Fellow (JRF)

NO. OF VACANCIE(S) - (01)

FELLOWSHIP: Rs. 16,000/- plus HRA

PROJECT DURATION: 2014-2016 (Two years)

LAST DATE FOR APPLICATION: Aug 18, 2014.

Eligibility criteria:

M.Sc./M.Tech./ in Biological Sciences/Biotechnology/Bio-Informatics. Candidates with research experience in the field of Drosophila/Yeast genetics will be preferred.

Application Procedure:

A covering letter along with your CV, copy of prior publications (if any) and proof of experience should be e-mailed to lmb_sau@aol.com. Hardcopy of the application should be brought on the day of interview along with other testimonials and marks statements for verification purpose.

IMPORTANT NOTE:

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

-SAU may select candidates against the post depending upon qualification and experience of candidates and reserves the right to relax any of the qualifications in case the candidate is found otherwise well qualified by the Selection Committee

-The abovementioned post is temporary and will be initially offered for a period of one year and can be extended, on satisfactory performance.

More at http://www.sau.ac.in/recruitment/vacancy.html

Metagenomic simulators are a way of dealing with this issue; they produce artificial sequencing datasets in which both the composition of the microorganisms and the expected results are known. Researchers can then test a pipeline on such a controlled dataset and see precisely how well it functions. However, as metagenomic studies have become larger, more diverse, and more complex, simply generating artificial reads is no longer sufficient. The simulators now have to replicate community variation, sequencing errors, different sequencing platforms, massive data volumes, and even laboratory-based biases.

MIDASim (2024) was designed with a particular emphasis on microbial community dynamics. Unlike previous tools which regarded each simulated sample as individual, MIDASim is able to efficiently generate realistic multi-sample microbiome datasets, covering the cases where changes over time are being tracked. This feature is particularly useful when investigating how microbial communities vary between people, different experimental setups, or at various times. By overcoming the computational limitations of earlier simulation methods, MIDASim has made it easier to carry out large and complex microbiome simulation studies.

A major challenge is scale. Since modern metagenomic projects can involve millions or even billions of sequencing reads, generating such large synthetic datasets can become a significant computational problem. In order to tackle this issue, Izzy (2025) was developed. As a high-throughput metagenomic read simulator, Izzy is designed with speed in mind while still reproducing the typical patterns of sequencing errors. The people who developed it stated that it can be as much as 60 times faster than earlier tools, which makes large-scale simulations far more practical. Now, researchers can begin to ask not how long a simulation will take but rather what size dataset they want to test.

At the same time, the sequencing technology became more diverse. Researchers were not any longer restricted to using Illumina short reads since Oxford Nanopore and PacBio long-read sequencing also became important in the field of metagenomic research. In order to address these new requirements, MeSS (Metagenomic Sequence Simulator, 2025) was developed. The programme is based on a Snakemake framework and is therefore compatible with the Illumina, Oxford Nanopore and PacBio platforms. MeSS has also been designed to operate efficiently and to use less memory than earlier tools; it provides ready-made templates for the microbiomes of different sites in the human body, thus giving researchers a simple means of beginning to generate realistic simulated communities.

The simulation problem became even more specialized. Suppose that sequencing is not based on uniform sampling of DNA? In the case of targeted sequencing and hybridization-capture experiments, particular sequences are deliberately enriched, and the probability of capturing a target depends on both the probe and the target sequence. A standard model based on uniform sampling might fail to take into account this important feature of real experiments. That is why RAmpSim has been designed specifically to handle simulations for capture-based and targeted sequencing. Instead of depending solely on the assumption of uniform sampling, it includes a thermodynamic nearest-neighbor energy model to represent probe–target interactions and sequence-dependent enrichment. As a result, it is especially suitable for applications such as hybridization capture in metagenomics, where the efficiency of recovering a sequence can depend strongly on how it relates to the capture probes. RAmpSim thus reflects a wider trend towards simulations that aim not only to reproduce sequencing output but also key aspects of the experimental process itself.

MIDASim, Izzy, MeSS and RAmpSim all demonstrate how fast metagenomic simulation is evolving. MIDASim is able to deal with realistic variation within a large number of and changing microbial communities. Izzy overcomes the problem of generating very large datasets. MeSS provides support for a number of sequencing technologies in an efficient and repeatable manner. RAmpSim increases the experimental realism for capture-based sequencing. Although each of these tools addresses a separate issue, they all contribute to advancing the field.

Modern metagenomic simulation therefore aims not only at producing artificial FASTQ files. Researchers nowadays desire simulated datasets that reflect community changes, incorporate the characteristics of the sequencing platform, include real error patterns, take into account computational scale, and account for experimental biases. As metagenomic workflows become more advanced, the simulators have to keep up with this development. The tools are now going beyond that of simple data generators; they produce controlled versions of complex metagenomic experiments and thus provide researchers with something that ordinary sequencing data seldom does: a dataset in which the answer is known before any analysis takes place.

Eligibility : MSc, M Phil / Phd, BE/B.Tech
Location : Himachal Pradesh-other
Job Category : Govt Jobs, Research, Walkin
Last Date : 20 Aug 2014

Advertisement No.6/2014

Post : Project Fellow
Research Associate/ Project Fellow Jobs opportunity in CSIR-Institute of Himalayan Bioresource Technology
M.Sc. in Bioinformatics/Computer Science with 55% marks and (ii) M.Sc. Bioinformatics/ Computational biology/ P.G. Diploma in Bioinformatics/B.Tech. or higher Degree in Bioinformatics with 55% marks

Date of Interview: 29.08.2014.

More at http://www.ihbt.res.in/recruit/AdvtNo6_2014.pdf

However, nanopore sequencing is an emerging and rapidly developing technology. It is not clear what will be most informative. We hope that IONiseR will provide a framework for visualisation of metrics that we haven’t thought of, and welcome feedback at mike.smith@embl.de.

If you’re not interested in the quality assement of the raw or event level data, and want to jump straight to the getting FASTQ format files from fast5 files you can go straight to the final section of this document.

Address of the bookmark: https://www.bioconductor.org/packages/devel/bioc/vignettes/IONiseR/inst/doc/IONiseR.html

more at https://ccb.jhu.edu/software/hisat2/index.shtml

Address of the bookmark: https://github.com/infphilo/hisat2

It installs in any computer even if you don't have administrator rights!

Address of the bookmark: http://www.dnabaser.com/download/DNA-Counter/index.html