Address of the bookmark: https://peerj.com/preprints/453.pdf

It demonstrates how to use long PacBio sequencing reads to assemble a bacterial genome, and includes additional steps for circularising, trimming, finding plasmids, and correcting the assembly with short-read Illumina data.

 Please comment if you know any other long read addembly tutorial.

Address of the bookmark: http://sepsis-omics.github.io/tutorials/modules/cmdline_assembly_v2/

ROLLING ADVERTISEMENT NO. 01/2014(E-1)
ADVERTISEMENT FOR THE POSITIONS OF ASSISTANT PROFESSOR CANDIDATES CAN APPLY ANY TIME DURING THE YEAR.

IIT Delhi invites applications from qualified Indian Nationals, Persons of Indian Origin (PIOs) and Overseas Citizens of India (OCIs) for the following positions in the various Departments/Centres/Schools (in the fields
mentioned alongwith them):
Post Pay Band Assistant Professor and Assistant Professor (on Contract) Rs.15600-39100 (PB-3) (Minimum pay of Rs.30000/-)+ AGP Rs.8000/-

The following norms will be followed for fixing the basic pay + AGP for Assistant Professors appointed on
contract with Ph.D but experience of 3 years or less:-
Type Qualification & Experience on the date of joining
Assistant Professor (Contract) PB3 (Rs. 15,600-39,100).

MINIMUM QUALIFICATIONS AND EXPERIENCE:
Ph.D. with First class at the preceding degree or equivalent in the appropriate branch with very good academic record throughout. A minimum of three years industrial/research/teaching experience, excluding however, the experience gained while Pursuing Ph. D. The candidates should preferably be below
35 years of age for male and 38 years for female ( to be relaxed by 5 years in case of persons with physical disability, SC/ST and 3 years in case of OBC-NCL).

Qualified persons include:
(a) Indian Nationals,
(b) Foreign Nationals who are “Persons of Indian Origin” (PIO) or Overseas
Citizens of India (OCI), in whose case, if selected, permission will be sought from Govt. of India
before he/she can join IIT Delhi, or
(c) Other Foreign Nationals, in whose case, if selected, appointment will be on a contract basis for up to 5 (five) years subject to permission from the Govt. of India before he/she can join IIT Delhi.
(d) Institute specifically encourages applicants from SC/ST/OBC category as well as persons
with disability to apply for these positions.

AMAR NATH & SHASHI KHOSLA SCHOOL OF INFORMATION TECHNOLOGY:
Computational Neuroscience, Medical Applications of Information Technologies, Computational & Systems Biology, Machine to Machine (M2M) Technologies, Embedded Systems & Sensors, Computer Security.
KUSUMA SCHOOL OF BIOLOGICAL SCIENCES:
In-silico Biology Applications, Systems Biology, Infection Biology, Neurodegeneration.

More at http://www.iitd.ac.in/sites/default/files/jobs/faculty/spl-areas-rolling-advt.pdf

http://www.iitd.ac.in/content/faculty-positions

Address of the bookmark: https://github.com/fenderglass/Flye

Apply now Job no: 494553
Work type: Continuing full time
Vacancy type: External Vacancy, Internal Vacancy
Categories: Academic - Teaching and Research

The Faculty of Science is launching a new and innovative branch of biological science at Macquarie University – Synthetic Biology. Synthetic biology combines engineering principles with molecular biological approaches to design and construct biological devices and systems. Recent highlights in this field include the design and synthesis of a functional bacterial genome and a yeast chromosome, and generation of synthetic bacterial cells. The rational synthesis of "designer" organisms yield important insights into how organisms work and has the potential to revolutionise biotechnological applications in areas such as bioenergy and biomanufacturing.

Find more at http://jobs.mq.edu.au/cw/en/job/494553/lecturersenior-lecturer-level-bc-in-synthetic-biology-research-fellow-level-b-in-synthetic-biology-lecturersenior-lecturer-level-bc-in-bioinformatics

https://academic.oup.com/nar/article/47/11/e63/5377471

Address of the bookmark: https://github.com/linzhi2013/MitoZ

Applicants are invited to send their resume and a recommendation letter to Prof. Patrick Meyer (more details at www.biosys.ulg.ac.be )

More at https://software.broadinstitute.org/gatk/download/bundle

ftp://ftp.ncbi.nlm.nih.gov/snp/organisms/human_9606/VCF/GATK/.

ftp://ftp.broadinstitute.org/bundle/hg38/hg38bundle/

Address of the bookmark: https://console.cloud.google.com/storage/browser/genomics-public-data/resources/broad/hg38/v0?pli=1

This job will allow the intern to become more familiar with new biological and bioinformatics tools like next generation sequencing, RNA-Seq data analysis and comparative genomics.

To apply for this position, send the following documents (in PDF format) to Dr Pierre-Yves Dupont (email p.y.dupont@massey.ac.nz):

1. A short cover letter.
2. A curriculum vitae, with transcript details.
3. The names and contact details of two referees willing to provide a confidential letter of recommendation upon request.

Informal enquiries are welcome. Formal applications are due by Sunday 2nd December 2012.
Requirements:

This position requires a good understanding of genetic problems, a good command of at least one scripting language (Perl, Python...), a basic knowledge of MySQL or any relational database management system. Knowledge in biological programming libraries (BioPython, BioPerl, BioRuby...), Java, C++ or any compiled language is an asset but not required. Undergraduate or Master degree is required.
Contact Information:

Dr. Pierre-Yves Dupont
Institute of Molecular BioSciences
Massey University
Private Bag 11 222
Palmerston North 4442
NEW ZEALAND

http://massey.genomicus.com/
p.y.dupont@massey.ac.nz

Information about the Institute of Molecular BioSciences (http://imbs.massey.ac.nz/) and the Computational Biology Research Group (http://massey.genomicus.com/) is available online. For more information about the position, you can contact Dr Pierre-Yves Dupont (email p.y.dupont@massey.ac.nz).

##################################################
[Mon May 7 11:29:18 2018] Reduction...
#file name genome size contigs heterozygous size [%] heterozygous contigs [%] identity [%] possible joins homozygous size [%] homozygous contigs [%]
/usr/lib/python2.7/dist-packages/matplotlib/font_manager.py:273: UserWarning: Matplotlib is building the font cache using fc-list. This may take a moment.
warnings.warn('Matplotlib is building the font cache using fc-list. This may take a moment.')
test/run1/contigs.fa 163897 245 66377 40.50 221 90.20 94.854 0 97520 59.50 24 9.80

##################################################
[Mon May 7 11:29:29 2018] Estimating parameters of libraries...
Aligning 19504 mates per library...
Insert size statistics Mates orientation stats
FastQ files read length median mean stdev FF FR RF RR
test/5000_1.fq.gz test/5000_2.fq.gz 50 4998 4990.20 721.47 0 4674 0 0
test/600_1.fq.gz test/600_2.fq.gz 100 599 598.63 47.68 0 10000 0 0

##################################################
[Mon May 7 11:29:29 2018] Scaffolding...
iteration 1.1: test/run1/contigs.reduced.fa 24 97520 39.355 17 94157 7321 2195 0 29603
19505 pairs. 17302 passed filtering [88.71%]. 1627 in different contigs [8.34%].
1526 pairs. 558 in different contigs [36.57%].
iteration 1.2: test/run1/_sspace.1.1.fa 3 97626 39.344 3 97626 87536 6063 821 87536
19505 pairs. 17607 passed filtering [90.27%]. 182 in different contigs [0.93%].
1077 pairs. 124 in different contigs [11.51%].
iteration 2.1: test/run1/_sspace.1.2.fa 3 97626 39.344 3 97626 87536 6063 821 87536
19505 pairs. 15112 passed filtering [77.48%]. 1295 in different contigs [6.64%].
3417 pairs. 396 in different contigs [11.59%].
iteration 2.2: test/run1/_sspace.2.1.fa 1 99133 39.344 1 99133 99133 99133 2328 99133
19505 pairs. 15152 passed filtering [77.68%]. 0 in different contigs [0.00%].
3398 pairs. 0 in different contigs [0.00%].

##################################################
[Mon May 7 11:29:34 2018] Gap closing...
iteration 1.1: test/run1/scaffolds.fa 1 99133 39.344 1 99133 99133 99133 2328 99133

##################################################
[Mon May 7 11:29:35 2018] Final reduction...
#file name genome size contigs heterozygous size [%] heterozygous contigs [%] identity [%] possible joins homozygous size [%] homozygous contigs [%]
[WARNING] Nothing reduced!
test/run1/scaffolds.filled.fa 99390 1 0 0.00 0 0.00 0.000 0 99390 100.00 1 100.00

##################################################
[Mon May 7 11:29:35 2018] Reporting statistics...
#fname contigs bases GC [%] contigs >1kb bases in contigs >1kb N50 N90 Ns longest
test/contigs.fa 245 163897 40.298 24 117391 3975 233 0 29603
test/run1/contigs.fa 245 163897 40.298 24 117391 3975 233 0 29603
test/run1/contigs.reduced.fa 24 97520 39.355 17 94157 7321 2195 0 29603
test/run1/_sspace.1.1.fa 3 97626 39.344 3 97626 87536 6063 821 87536
test/run1/_sspace.1.2.fa 3 97626 39.344 3 97626 87536 6063 821 87536
test/run1/_sspace.2.1.fa 1 99133 39.344 1 99133 99133 99133 2328 99133
test/run1/_sspace.2.2.fa 1 99133 39.344 1 99133 99133 99133 2328 99133
test/run1/scaffolds.fa 1 99133 39.344 1 99133 99133 99133 2328 99133
test/run1/_gapcloser.1.1.fa 1 99390 39.689 1 99390 99390 99390 2 99390
test/run1/scaffolds.filled.fa 1 99390 39.689 1 99390 99390 99390 2 99390
test/run1/scaffolds.reduced.fa 1 99390 39.689 1 99390 99390 99390 2 99390

##################################################
[Mon May 7 11:29:35 2018] Cleaning-up...
#Time elapsed: 0:00:17.376924