python finisherSC.py destinedFolder mummerPath

If you are running on server computer and would like to use multiple threads, then the following commands can generate 20 threads to run FinisherSC.

python finisherSC.py -par 20 destinedFolder mummerPath

Sometimes, if the names of raw reads and contigs consists of special characters/formats, FinisherSC/MUMmer may not parse them correctly. In that case, you want to have a quick renaming of the names of contigs/reads in contigs.fasta or raw_reads.fasta using the following command.

    perl -pe 's/>[^\$]*$/">Seg" . ++$n ."\n"/ge' raw_reads.fasta > newRaw_reads.fasta
    cp newRaw_reads.fasta raw_reads.fasta
    perl -pe 's/>[^\$]*$/">Seg" . ++$n ."\n"/ge' contigs.fasta > newContigs.fasta
    cp newContigs.fasta contigs.fasta

Address of the bookmark: https://github.com/kakitone/finishingTool

Project entitled: "Establish of Bioinformatics Facility for biology teaching through bioinformatics"

Name of post: Research Associate /Trainees

Number of post: 03

Educational Qualification and Experience: Candidates should have Ph D in relevant subjects with experience in handling computational biology resources and software

Selection mode: Walk in interview

How to apply?
Interested and eligible candidates may appear for a walk-in interview on 14th November 2015 at 11.00 am, in the office of Director, Centre for Bioinformatics along with CV and attested copies of all testimonials and additional qualifications.

Recruitment reference: http://www.mdurohtak.ac.in/pdf/career/adv_research_asso_dbt_bioinfo.pdf

conda install -c atgc-montpellier lorma

Address of the bookmark: https://gite.lirmm.fr/lorma/lorma-releases/wikis/home

Rajiv Gandhi Centre for Biotechnology (RGCB) invites applications for the following three faculty scientist positions:

Scientist G in any of the following disciplines of disease biology: Cancer Research/Cardiovascular Biology/Diabetes Biology/Pathogen Biology
Scientist E-II or F in Bioinformatics & Computational Biology
Scientist E-I or E-II in Cancer Research with special emphasis on Human Papillomavirus Research

More at http://rgcb.res.in/wp-content/uploads/2015/11/APPLICATION-FORMAT-FOR-SCIENTISTS.docx

Address of the bookmark: https://github.com/ruanjue/wtdbg2

More at

https://www.isas.de/files/redaktion/jobs/2021/18.60.1_Postdoc_deNBI_06_21_AS.pdf

https://www.isas.de/en/news/062021-post-doctoral-position-scientist-mfd-in-bioinformatics

~$ ./sviper -s short-reads.bam -l long-reads.bam -r ref.fa -c variants.vcf -o polished_variants

This will output a polished_variants.vcf file, that contains all the refined variants.

Sometimes it is helpful to look at the polished sequence, e.g. with the IGV browser. In that case you want SViper to output the polished and aligned sequences in a bam file via the option --output-polished-bam:

~$ ./sviper -s short-reads.bam -l long-reads.bam -r ref.fa -c variants.vcf -o polished_variants --output-polished-bam

Address of the bookmark: https://github.com/smehringer/SViper

A full-time post-doctoral position for a bioinformatician with experience in managing and analyzing NGS data is available in the Laboratory of Molecular Cardiology at Policlinico San Donato-IRCCS, Milan, Italy. For lab publications, see: http://scholar.google.it/citations?user=wAPKO9wAAAAJ&hl=it&oi=ao

https://www.researchgate.net/profile/Fabio_Martelli

The goal of the project is investigating the regulation and functional role of non coding RNAs in tissue response to hypoxia and ischemia.

We are looking for a candidate that is going to interact with biologists and bioinformaticians to manage and analyze NGS data (mostly RNA-seq) and microarray data.

The successful candidate must have a minimum of 3 years experience in dealing with NGS data, a good command of English and written communication and at least 2 relevant publications as first author in peer reviewed international journals. The candidate is expected to interact with a small international group and to be able also to work independently. Knowledge of programming is a definitive plus, as well as a good statistical background and/or wet molecular biology skills.

Salary is proportional to experience and to the publication record (up to 38 000euro/year before taxes and retirement contribution i.e. IRPEF and INPS).

Please, send your CV by e-mail to Fabio Martelli:

fabio.martelli@grupposandonato.it

Location: Laboratory of Molecular Cardiology at Policlinico San Donato-IRCCS, Milan, Italy.
Link: https://www.researchgate.net/profile/Fabio_Martelli
Contact person: Fabio Martelli
Contact email: fabio.martelli@grupposandonato.it

https://www.darwintreeoflife.org/an-initial-set-of-raw-genome-assemblies-from-the-darwin-tree-of-life-project/

Address of the bookmark: https://www.darwintreeoflife.org/an-initial-set-of-raw-genome-assemblies-from-the-darwin-tree-of-life-project/

Project Title : "Targeting TAL effector mediated susceptibility for durable and broad-spectrum resistance to bacterial blight in Rice"

No. of Post : 01

Qualification : MSc in any subject under Life Science or Bioinformatics/ B.Tech in Bioinformatics + 1 yr experience

Stipend : Rs. 14,000/-

How to apply

Interested candidates are requested to send their applications explaining their interest in the position with an updated CV to Dr. Ginny Antony, Assistant Professor, Department of Plant Science, School of Biological Sciences, Central University of Kerala, Padannakkad, Kasaragod, Kerala - 671 314 email: ginnycuk2013@gmail.com on or before 20th December, 2015.

More at http://cukerala.ac.in/index.php?option=com_content&view=article&id=1022:applications-invited-for-the-post-of-jrf-department-of-plant-science&catid=106&Itemid=593&lang=en