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)

Chettinad Academy of Research and Education (CARE) invites applications from eligible and translational research-oriented candidates to the posts of Professor/Associate Professor/ Assistant Professor Computational Biology, Bioinformatics, and Pharmaceutical Chemistry.

Emoluments: As per UGC norms (Adequate Compensation for Postdoctoral/Teaching experience)

Candidates fulfilling the eligibility criteria as per the UGC norms can send their full CV with copies of certificates and reference letters to the following address by post or by e-mail on or before 31st May 2014

The Registrar,
Chettinad Academy of Research and Education,
Chettinad Health City
Kelambakkam, Chennai 603 103
Tamil Nadu
T +91 (0)44 4741 1000
F +91 (0)44 4741 1011
Email: jobs @chettinadhealthcity.com

Advertisement: http://182.73.176.163/chc/ads2014.pdf

https://github.com/kakitone/MetaFinisherSC

https://github.com/kakitone/BIGMAC

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

http://www.eva.mpg.de/genetics/bioinformatics/overview.html?Fsize=0%2C%20%40%2F%27

Kelso Group
Department of Evolutionary Genetics
Max Planck Institute for Evolutionary Anthropology
Deutscher Platz 6
04103 Leipzig
Germany
Phone: +49 341 3550 500

Job:
http://www.eva.mpg.de/genetics/bioinformatics/jobs.html?Fsize=0%2C%2B%40

• FracMinHash sketching, which enables accurate comparisons (including ANI) between data sets of different sizes
• sourmash gather, a combinatorial k-mer approach for more accurate metagenomic profiling

Please see the sourmash publications for details.

The name is a riff off of Mash, combined with @ctb's love of whiskey. (Sour mash is used in making whiskey.)

Maintainers: C. Titus Brown (@ctb), Luiz C. Irber, Jr (@luizirber), and N. Tessa Pierce-Ward (@bluegenes).

sourmash was initially developed by the Lab for Data-Intensive Biology at the UC Davis School of Veterinary Medicine, and now includes contributions from the global research and developer community.

Address of the bookmark: https://github.com/sourmash-bio/sourmash

Tasks:  239 total,   1 running,  238 sleeping,   0 stopped,   0 zombie

This line tells you how many processes are running. If you are using laptops machines it’s not so interesting because you really are the only one using this machine.

Cpu(s):  0.0%us,  0.0%sy,  0.0%ni,100.0%id,  0.0%wa,  0.0%hi,  0.0%si,  0.0%st

This line contains the CPU load. The first two numbers are how busy the system is doing computation (“us” stands for “user”) and how busy the system is doing system-y things like accessing disks or network (“sy” stands for “system”). We’ll talk more about this later.

Mem:   49457320k total,    3492174k used,  14535596k free,    1435148k buffers

This should be easy to understand – how much memory you’re using!

Swap:   539356k total,   28332k used,   836562k free,    29862014k cached

Swap is just on-disk memory that can be used to “swap” out programs from main memory. Again, we’ll talk about this later.:

PID USER      PR  NI  VIRT  RES  SHR S %CPU %MEM    TIME+  COMMAND
  1 root      39   19  0  0  0 S  0.0  0.0   246:57.22 kipmi0
  2 root      RT   0     0    0    0 S  0.0  0.0   0:00.00 migration/0

And... finally! What’s actually running! The two most important numbers are the %CPU and %MEM towards the right, as well as the COMMAND. This tells you how compute- and memory-intensive your program is. Right now, nothing’s running so the numbers aren’t very interesting, but just wait until we run something...

This bookmark is created to provide NGS online books links.

Address of the bookmark: http://en.wikibooks.org/wiki/Next_Generation_Sequencing_%28NGS%29/Print_version

Assistant Professor in Bioinformatics

Essential :
First Class Master’s Degree in the appropriate branch of Life Sciences / Technology (Tech.)
OR
Ph.D in Life Sciences or in the respective subject area of specialization
OR
Good Academic record with at least 55% marks (or an equivalent grade) at the Master’s Degree level, in the relevant subject or an equivalent degree from an Indian / Foreign University.
Besides fulfilling the above qualifications, candidates should have cleared the eligibility test (NET) for lecturers conducted by the UGC, CSIR or similar test accredited by the UGC and as per the requirements of UGC guidelines.

Desirable :
Teaching, research industrial and/or professional experience in a reputed organization.
Papers presented at Conferences and/or in refereed journals

Note : Application are invited in prescribed form Click here for Application Form
Kindly send your applications to “Registrar, Dr. D. Y. Patil Vidyapeeth, Pune, Sant Tukaram Nagar, Pimpri, Pune – 411018., Maharashtra, India.” should reach in the University office within 15 days from the publication.

More Info: http://www.dpu.edu.in/BiotechResearchPositions.aspx

The work in our lab has focussed on computational approaches to speed-up the finishing process. Specifically, we have explored the use of optical mapping and mate-pair data to augment assemblies and direct finishing experiments. The tools developed in our lab have been used in several finishing projects, producing complete genomes (and near-complete ones) with surprisingly little computational and experimental effort (Nagarajan et al., in submission). The executables (as well as source code) for these tools are freely available here:

• Scaffolding using Optical Restriction Mapping
  Optical Maps are global, ordered maps of restriction site locations in a genome. This information can be quite useful in scaffolding contigs from a shotgun assembly to guide the finishing process. A set of programs to exploit optical maps for assembly can be found here: SOMA v2.0 (63 MB tar.gz file). This version of SOMA contains several improvements to programs in v1.0 as well as new scripts for working with multiple maps, contig graphs and scaffolds. 
  
  
• Augmenting assemblies with mate-pair data
  Mate-pair information can be valuable in augmenting short-read assemblies and reconstructing the genome as larger scaffolds. AMOS-Hybrid is a pipeline written in the AMOS framework (open-source assembly tools) to merge arbitrary mated reads into an existing assembly and merge contigs and create scaffolds where possible. Source code and executables for AMOS-Hybrid are available here: AMOS-Hybrid v1.0 (142 MB tar.gz file). 
  
  
• Assembly and sequence-composition guided finishing
  Contigs from a shotgun assembly are typically linked together in a graph structure that can serve to guide finishing and in some case close gaps in-silico. Also, in many cases, sequence composition of contigs can provide clues to fill gaps in scaffolds. A set of scripts to automate some of these tasks can be found here: Finishing Scripts v1.0 (63 MB tar.gz file). 

http://www.cbcb.umd.edu/finishing/

Address of the bookmark: http://www.cbcb.umd.edu/finishing/