https://www.bioconductor.org/packages/devel/bioc/vignettes/maftools/inst/doc/maftools.html

Address of the bookmark: https://github.com/PoisonAlien/maftools

Appointment Adv.No.2

Applications in plain paper are invited from Indian citizens for one/two position each of Research Associate, Traineeship and Studentship for BIF facility, Division of Life Sciences, IASST.

Applications with complete Bio-data containing contact address, e-mail and phone number, two recent passport size photographs and attested copies of mark sheets, certificates etc., should be sent to the Registrar, IASST, Paschim Boragaon, Garchuk, Guwahati – 781035, Assam, so as to reach on or before 5/05/2014.

A. Research Associate:

Number of vacancies: 1 (One)

Qualifications:

PhD in Bioinformatics or allied disciplines with knowledge of Bioinformatics. The candidates who have submitted PhD thesis may also apply.

In case, candidates having PhD are not found, candidates having MSc in Bioinformatics or allied disciplines with sound knowledge of Bioinformatics will be preferred.

Remuneration: Candidate having PhD will get a consolidated remuneration of Rs. 22,000/- +HRA per month. MSc having NET/GATE/SLET qualified candidate will get a remuneration of Rs. 16,000/= and HRA and candidate with only MSc will get a remuneration of Rs.14,000/- and HRA.

Tenure:

The post is initially for one year and may be extended depending on the performance till the tenure of the project.

B. Traineeship:

Number of vacancies: 2 (Two)

Qualifications:

Candidate with a postgraduate degree in Bioinformatics/Biotechnology/Life sciences from a recognised University

Remuneration: Rs. 5000/month for 6 months

C. Studentship:

Number of vacancies: 2 (Two)

Qualifications:

Candidate pursuing M.Sc in bioinformatics in a recognised University.

Remuneration: Rs. 5000/month for 6 months

Advertisement:

http://iasst.gov.in/pdf/recruitment/advt%20no_2_24042014.pdf

You can try this here, or try it later on your own data.

Get data

We will use the same Illumina data as we used above:

• illumina_R1.fastq.gz: the Illumina forward reads
• illumina_R2.fastq.gz: the Illumina reverse reads

Assemble

Run Spades:

spades.py -1 illumina_R1.fastq.gz -2 illumina_R2.fastq.gz --careful --cov-cutoff auto -o spades_assembly_all_illumina

• -1 is input file of forward reads
• -2 is input file of reverse reads
• --careful minimizes mismatches and short indels
• --cov-cutoff auto computes the coverage threshold (rather than the default setting, “off”)
• -o is the output directory

Results

Move into the output directory and look at the contigs:

infoseq contigs.fasta

Now, two research groups have engineered new optogenetic proteins that can be used to efficiently silence neurons. One of the two new proteins comes from the lab of Karl Deisseroth, a psychiatrist and neuroscientist at Stanford University who helped develop optogenetics as a research tool. His group’s new “off” switch for neurons was created by changing 10 of the 333 amino acids in an existing optogenetic protein, which itself had been engineered by combining natural proteins from green algae. That advance “creates a powerful tool that allows neuroscientists to apply a brake in any specific circuit with millisecond precision,” said Thomas Insel, director of the National Institute of Mental Health, in a released statement. The other new silencing protein, developed by scientists at the Humboldt University of Berlin and collaborators, was created by changing amino acids in the same existing optogenetic protein. 

Some researchers are also looking to optogenetics as a potential treatment for patients with a variety of conditions (see “For Mice, and Maybe Men, Pain Is Gone in a Flash,” and “Flipping on the Lights to Halt Seizures”) but there are huge challenges to overcome. The method requires genetic modification of cells to make them light-sensitive. It also requires implanted light sources for all but the shallowest of nerve endings.

Smudgeplots are computed from raw or even better from trimmed reads and show the haplotype structure using heterozygous kmer pairs. For example:

Address of the bookmark: https://github.com/KamilSJaron/smudgeplot

Address of the bookmark: https://www.ncbi.nlm.nih.gov/nuccore/ON563414

SCHOOL OF COMPUTATIONAL AND INTEGRATIVE SCIENCES (SC&IS)

ESSENTIAL QUALIFICATION : - M.Sc./M.Tech. in Physics/ Chemistry/ Biology/ Mathematics/ Statistics/ Bioinformatics/ Computational Biology. Ph.D. in the broad areas of Bioinformatics/ Computational Biology. Candidates must have demonstrated capabilities in terms of high impact research publications in either of the above mentioned areas.

Scale of Pay : - 15600-39100/- (PB-III) AGP Rs. 6000/-

For more details on Centre/School, Specializations etc. please visit JNU website www.jnu.ac.in or contact Section Officer, Room Nos. 131-132, Recruitment Cell, Administrative Block, JNU, New Delhi – 110067, Email: recruitmentjnu2013@gmail.com The last date for the receipt of application is 15 May, 2014.

http://www.jnu.ac.in/Career/

http://www.jnu.ac.in/Career/ADVTNo_RC_48_2014.pdf
Last Apply Date:

15 May 2014

What is PhyloHerb: PhyloHerb is a wrapper program to process genome skimming data collected from plant materials. The outcomes include the plastid genome (plastome) assemblies, mitochondrial genome assemblies, nuclear ribosomal DNAs (NTS+ETS+18S+ITS1+5.8S+ITS2+28S), alignments of gene and intergenic regions, and a species tree. It is designed to be a high throughput program dealing with lower quality data. Examples include low-coverage (5x cpDNA) plastome phylogeny, recycling plastid genes from target enrichment data, retrieving low-copy nuclear genes from medium coverage (5x nucDNA) genome skimming.

License: GNU General Public License

Citation:

• Cai, Liming, Hongrui Zhang, and Charles C. Davis. 2022. PhyloHerb: A high‐throughput phylogenomic pipeline for processing genome‐skimming data. Applications in Plant Sciences 10(3): 1–9. https://doi.org/10.1002/aps3.11475

Address of the bookmark: https://github.com/lmcai/PhyloHerb/