Mandatory requirements
Knowledge of #Python,#PERL,#R (one or more) and shell environment (#linux )
Knowledge about database - #mysql, #oracle, #mongodb (one or more)
Past industry experience >= 2 years or equivalent

Other skill sets
Knowledge of #nextflow and/or #snakemake
Basic knowledge of bioinformatics/genomics

Send your applications to careers@medgenome.com

Adapter sequences:
Optimal enzymes for amplifying sequencing libraries.
Quail, M. a et al. Nat. Methods 9, 10-1 (2012).

GAGE:
GAGE: A critical evaluation of genome assemblies and assembly algorithms.
Salzberg, S. L. et al. Genome Res. 22, 557-67 (2012).

KMC:
Disk-based k-mer counting on a PC.
Deorowicz, S., Debudaj-Grabysz, A. & Grabowski, S. BMC Bioinformatics 14, 160 (2013).

Kraken:
Kraken: ultrafast metagenomic sequence classification using exact alignments.
Wood, D. E. & Salzberg, S. L. Genome Biol. 15, R46 (2014).

MUMmer:
Versatile and open software for comparing large genomes.
Kurtz, S. et al. Genome Biol. 5, R12 (2004).

R:
R: A language and environment for statistical computing.
R Core Team (2013). R Foundation for Statistical Computing, Vienna, Austria. URL http://www.R-project.org/.

RATT:
RATT: Rapid Annotation Transfer Tool.
Otto, T. D., Dillon, G. P., Degrave, W. S. & Berriman, M. Nucleic Acids Res. 39, e57 (2011).

SAMtools:
The Sequence Alignment/Map format and SAMtools.
Li, H. et al. Bioinformatics 25, 2078-9 (2009).

Trimmomatic:
Trimmomatic: A flexible trimmer for Illumina Sequence Data.
Bolger, A. M., Lohse, M. & Usadel, B. Bioinformatics 1-7 (2014).

Postdoc position (m/w/d)

in the field of computational evolutionary microbiology is available
for an initially limited period of 36 months at the earliest possible
date. The weekly working time corresponds to 100% of full employment
(If the legal requirements under collective bargaining law are met, the
tariff grouping is carried out up to pay scale 13 TV-L. The obligation
to teach amounts to 4 hours.

The Genomic Microbiology Group research interests are focused on
microbial genome evolution with an emphasis on the study of lateral gene
transfer. In our research we use both computational and experimental
approaches (see www.uni-kiel.de/genomik). The position offers the
opportunity to develop an independent research profile within the group
research focus. The successful applicant is expected to be involved
in teaching of bioinformatics and molecular evolution, including the
development of teaching materials (lectures/exercises/short videos).

Your profile:
· Doctoral or PhD degree in Molecular Evolution, Bioinformatics or
related fields.
· Knowledge and experience in programming (e.g., Python) and
biostatistical analysis (e.g., with R or MatLab).
· Any of the following expertise is an advantage: the analysis of
genomic or transcriptomic data, phylogenetic reconstruction,
comparative genomics.
· Good oral and written communication skills in English.
· Ability to teach in German is an advantage (alternatively, an
indication to do so from the 2nd year on).
· Skills and motivation to communicate and interact with other
scientists.

The Christian-Albrechts-University sees itself as a modern and
cosmopolitan employer. We welcome your application regardless of your age,
gender, cultural and social background, religion, ideology, disability
or sexual identity. We promote equality of the sexes.

The Christian-Albrechts-University is committed to the employment of
people with disabilities. Preference will be given to applications from
severely handicapped persons and persons of equal standing, provided
they are suitable.

We expressly welcome applications from people with a migration background.

For enquiries regarding the position, teaching obligations and research
topic please contact Prof. Tal Dagan: tdagan@ifam.uni-kiel.de.

Applications should be submitted by email to Mrs. Haacks
(dhaacks@ifam.uni-kiel.de) as a single PDF and include: (1) a letter of
motivation (max 1 page, Arial 11, line spacing 1.15), (2) CV, (3) PhD
certificate. Please use 'GMG postdoc application - [your name]'
as a subject.

Please, refrain from sending us application photos.

Application deadline: August 31 2021 or until the position is
filled. Interviews will take place during September/October 2021. The
planned starting date for the position is flexible (but in 2021).

Like other indel callers, Scalpel works by performing de novo assembly of regions of interest, so that misalignment to the reference genome cannot obscure the presence of an insertion or deletion. Scalpel's innovation is to repeatedly check its assembly before comparing to the reference genome, to account for simple sequence repeats that are a regular source of error in indel calling. When Scalpel assembles an exon, it collects reads that map to that exon (including partial matches), splits them into k-mers, and creates a de Bruijn graph to span the exon; however, if it detects repeats in the map, it iteratively increases the size of the k-mers by one base until the repeats are eliminated. This ensures that the final assembly of the exon is highly accurate while minimizing compute time.

The Cold Spring Harbor team's validation of Scalpel, published over the weekend in Nature Methods, compares Scalpel's performance on a live whole exome against HaplotypeCaller and SOAPindel. The donor is an individual with serious neurological disorders, which may be linked to a high incidence of indels. One thousand indels from this individual's exome, called by one or more of the informatics pipelines, were selected for focused resequencing. This resequencing revealed a 77% true positive rate for Scalpel calls, dramatically better than the rates for either of the competing tools; Scalpel performed especially well with indels longer than five base pairs, a traditional weak point for indel callers.

Finally, the authors demonstrate Scalpel's use on a large set of genetic data from nearly 600 families who donated samples to the Simons Simplex Collection, a project of the Simons Foundation Autism Research Initiative. Scalpel found a very high enrichment for indels in children affected by autism, compared with their unaffected siblings, a pattern that persisted even after excluding common variants.

The pipeline is built using Nextflow, a workflow tool to run tasks across multiple compute infrastructures in a very portable manner. It uses Docker/Singularity containers making installation trivial and results highly reproducible. The Nextflow DSL2 implementation of this pipeline uses one container per process which makes it much easier to maintain and update software dependencies.

Address of the bookmark: https://github.com/AusARG/pipesnake

Why Bioinformatics Matters More Than Ever

Every day, our world generates massive amounts of biological data—from genome sequences to microbiome profiles to real-time pathogen surveillance. Hidden within these datasets are the answers to some of the greatest challenges humanity faces: emerging diseases, antimicrobial resistance, environmental stress, genetic disorders, sustainable agriculture, and more.

Bioinformatics isn’t just a skill.
It’s the language of the future of biology.

By mastering it, you give yourself the power to:

Decode genomes and understand life at its most fundamental level

Identify patterns no microscope could ever reveal

Predict disease outbreaks before they occur

Accelerate drug discovery with computational precision

Contribute to open-source tools that empower scientists worldwide

You don’t just follow science—you drive it.

Every Expert Was Once a Beginner

Many newcomers feel intimidated. Command-line interfaces. R scripts. Python packages. Next-generation sequencing data. Complex machine learning models.

But here’s the truth: every bioinformatician started exactly where you are now—curious, unsure, but excited.

No one writes perfect code on day one.

No one understands genomics pipelines immediately.

What makes you a bioinformatician is not perfection, but perseverance.

When your script throws a cryptic error…
When your data refuses to format…
When your pipeline runs for 6 hours only to crash…

Remember: this is part of the journey.
Every error teaches you. Every retry strengthens you. Every breakthrough energizes you.

Bioinformatics Is Not Just a Career—It’s a Mindset

It’s the mindset of:

Problem-solving.

Continuous learning.

Turning chaos into clarity.

Seeing what others can’t.

Bioinformaticians are detectives of biological complexity. You sit at the intersection of innovation, using tools that can shape public health, medicine, agriculture, and ecology. Few fields give you such direct impact on the world.

Your Contribution Matters

As you work on your script, pipeline, genome, or model, remember:

Somewhere, your analysis might contribute to:

A new therapy

A faster diagnostic test

A better understanding of a pathogen

A more resilient crop

An open-source dataset that helps thousands

A discovery that rewrites textbooks

Your code may be small, but its ripple effect is powerful.

The Future Is Bioinformatics—And You Are Part of It

The world is shifting. Wet labs are integrating AI. Hospitals rely on genomic insights. Farmers use gene-level predictions. Governments monitor disease in real time. Students launch pipelines that become global tools.

This is a golden era—and you are not late.
You are exactly where you need to be.

Keep Pushing. Keep Learning. Keep Discovering.

Bioinformatics is a journey filled with challenges, but also with unmatched rewards.

So the next time you feel stuck, frustrated, or overwhelmed, remember:
You’re building the science of tomorrow.

Be proud. Stay curious. Keep going.
Your work matters more than you think.

More at http://www.doc.ic.ac.uk/~natasha/index.html

NEW DELHI-110067

Applications are invited for the position of Research Associate (RA) for the following time-bound sponsored project as per the details given below:

1. BTIS project entitled, “National Infrastructural Facility in the Area of Immunology” funded by DBT

Research Associate (One Position only)

Dr. Debasisa Mohanty Staff Scientist-VI deb@nii.res.in

Educational Qualifications: Ph.D in Bioinformatics or Biological Sciences or Biotechnology with research experience and publication record in indexed peer reviewed journals in the area of bioinformatics or computational biology.

Emoluments: The selected candidates will draw consolidated emoluments as per Institute Rules, depending upon qualifications & experience Research Associate: Rs. 36,000/- per month plus 30% HRA

Job description & Desired Knowledge: The candidate should be well versed in Programming in PERL/C++, HTML, CGI, web sever and portal development, computational analysis of protein structure & function, molecular dynamics simulations and use of high performance computing systems.

General Terms & Conditions:-

1. The candidates selected for the above posts will be on contract for one year or duration of the project whichever is shorter, at a time.

2. No hostel/ housing facility will be provided.

3. Applicants may clearly mention the category they belong to i.e. SC/ST/OBC/PH and attach documentary proof of the same.

4. No TA/DA will be paid for attending the interview, if called for.

5. Apart from sending application in the prescribed format given below, candidates should send complete Curriculum Vitae along with the names of three referees. Curriculum Vitae should contain details of the experimental expertise and list of publications. 6. Canvassing in any form will be a disqualification.

HOW TO APPLY Interested candidates may apply directly, STRICTLY IN THE PRESCRIBED FORMAT GIVEN BELOW, through e-mail, to the Investigator of the project, clearly indicating the name of the project along with their complete C.V., Email ID, fax numbers, telephone numbers. Only Short listed candidates will be called for interview and they required to submit attested copies of all their certificates and a Demand Draft of Rs 100/- drawn on Canara Bank or Indian Bank payable at Delhi/New Delhi in favour of the Director, NII (SC/ST/PH and Women candidates are exempted from payment of fees) subject to submission of documentary proof), at the time of interview. (E-MAIL APPLICATIONS SHOULD MENTION BTIS-RA 2015 IN THE SUBJECT LINE)

LAST DATE OF RECEIPT OF APPLICATIONS: 29th October, 2015

Advertisement:

www1.nii.res.in/sites/default/files/projectappointments-Dr.Mohanty-29oct2015.pdf

##################################################
[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

C. Titus Brown http://video.open-bio.org/video/1/a-history-of-bioinformatics-in-the-year-2039