BOL: Related items

CAMSA :: a tool for Comparative Analysis and Merging of Scaffold Assemblies

Rahul Nayak — Thu, 28 Dec 2017 09:10:26 -0600

CAMSA – is a tool for Comparative Analysis and Merging of Scaffold Assemblies, distributed both as a standalone software package and as Python library under the MIT license.

Main features:

works with any number of scaffold assemblies in de-novo non-progressive fashion
allows to simultaneously work with scaffold assemblies obtained from any in silico and in vitro techniques, supporting multiple existing formats via built-in converters
creates an extensive report with several comparative quality metrics (both on assembly level and on the level of individual assembly points)
constructs a merged combined scaffold assembly
provides an interactive framework for a visual comparative analysis of the given assemblies

Address of the bookmark: https://cblab.org/camsa/

Walk in for Research Asst & Programmer Enterovirus Research Centre Mumbai - India

Tue, 14 Apr 2015 12:36:51 -0500

Enterovirus Research Centre Mumbai Jobs 2015 –

Walk in for Research Asst & Programmer Posts: Enterovirus Research Centre, Mumbai, Indian Council of Medical Research has issued notification for the recruitment of Research Asst & Programmer vacancies on temporary basis for the project entitled “An Atlas of Non-Polio Enterovirus Types Isolated from Cases of Acute Flaccid Paralysis in India”. Eligible candidates may walk in on 20-04-2015 from 10:00 AM to 12:00 Noon. Other details like age limit, educational qualification, how to apply are given below…

Enterovirus Research Centre Mumbai Vacancy Details:
Total No. of Posts: 04
Name of the Posts:
1. Research Assistant: 03 Posts
2. Programmer: 01 Post

Age Limit: Candidates age should below 28 years. Age relaxations are applicable as per rules.

Educational Qualification: Candidates should have M.Sc (1st Class) in Microbiology/ Bioinformatics/ Biotechnology/ Life Science for post 1, BE/ B.Tech/ MCA for post 2.

Selection Process: Candidates are selected based on their performance in interview.

How to Apply: Eligible candidates may attend for interview along with original certificates, CV, attested copies of relevant certificates, one recent passport size photograph duly affixed on right side of application at Enterovirus Research Centre, Mumbai, Indian Council of Medical Research, Haffkine Institute Cmpound, Acharya Donde Marg, Parel, Mumbai-400012 on 20-04-2015 from 10:00 AM to 12:00 Noon.

Important Dates:
Date & Time of Interview: 20-04-2015 from 10:00 AM to 12:00 Noon.
Registration Time: 12:00 Noon.

TAREAN: A computational tool for identification and characterization of satellite DNA from unassembled short reads

Surabhi Chaudhary — Tue, 15 May 2018 02:53:11 -0500

TAndem REpeat ANalyzer -TAREAN – is a computational pipeline for unsupervised identification of satellite repeats from unassembled sequence reads. The pipeline uses low-pass whole genome sequence reads and performs their graph-based clustering. Resulting clusters, representing all types of repeats, are then examined for the presence of circular structures and putative satellite repeats are reported.

How to use TAREAN:

Install a local instance of the pipeline using its source code available from bitbucket repository.
Use public Galaxy-based server at https://repeatexplorer-elixir.cerit-sc.cz/. The server is provided in frame of the Elixir CZ project and is maintained by CESNET and CERIT-SC. Simple registration is required to use this service.

Development of TAREAN was supported by ELIXIR CZ research infrastructure project (MEYS Grant No: LM2015047).

References

Novak, P., Avila Robledillo, L., Koblizkova, A., Vrbova, I., Neumann, P., Macas, J. (2017) – TAREAN: a computational tool for identification and characterization of satellite DNA from unassembled short reads. Nucleic Acids Res., doi:10.1093/nar/gkx257

Address of the bookmark: https://bitbucket.org/petrnovak/repex_tarean

BINC Sample Question Paper !!!

Jitendra Narayan — Thu, 16 Apr 2015 09:15:09 -0500

BINC sample question paper round THREE ...

“One code to find them all”: a perl tool to conveniently parse RepeatMasker output files

Poonam Mahapatra — Mon, 04 Jun 2018 03:45:15 -0500

One code to find them all is a set of perl scripts to extract useful information from RepeatMasker about transposable elements, retrieve their sequences and get some quantitative information. Assemble RepeatMasker hits into complete TE copies, including LTR-retrotransposon Retrieve corresponding TE sequences, and flanking sequences, from the local fasta files Compute summary statistics for each TE family (number of TE copies, genome coverage...) Ambiguous cases such as nested TE can be assembled into copies automatically or manually Allow for working with a TE user-defined library Allow for working with only a user-chosen set of TE families http://doua.prabi.fr/software/one-code-to-find-them-all

Address of the bookmark: http://doua.prabi.fr/software/one-code-to-find-them-all

Senior Research Fellow (SRF) Bioinformatics at Central Institute for Research on Buffaloes

Sat, 18 Apr 2015 04:30:47 -0500

Senior Research Fellow (SRF) Bioinformatics at Central Institute for Research on Buffaloes
Address: Central Institute for Research on Buffaloes, Sirsa Road, Hisar
State: Haryana
Pay Scale: Post Graduate in subjects other than Veterinary Science Rs. 16000/- per month for 1st and 2nd year and Rs. 18000/- per month for 3rd year. Post Graduate in Veterinary Science Rs. 18000/- per month for 1st and 2nd Year and Rs. 20000/- per month for 3rd year.
Educational Requirements: Master’s degree in biotechnology/animal biotechnology, veterinary/animal biochemistry, veterinary microbiology or veterinary/animal physiology/Nano Technology/Bioinformatics or related area.
Qualifications: Ph.D in relevant field/experience of working in any research project
Details will be available at: http://www.cirb.res.in/attachments/195_Walk-in-Interview%20for%20Senior%20Research%20Fellow%20%28SRF%29%20%28On%20Dated%2020.4.2015%29.pdf
How To Apply: Interested candidates who fulfill the above conditions should report for interview with a copy of their bio-data, photocopy and original certificates and testimonials, other related material i.e. reports, documents, articles, etc., if any.
Date & Time of Interview: 20.04.2015 at 11.00 hrs
Venue: CIRB, Hisar

LSC :a long read error correction tool

Jit — Thu, 02 Aug 2018 07:39:46 -0500

Getting Started

These simple steps will help you integrate LSC into your transcriptomics analysis pipeline.

Read the LSC_requirements for running LSC.
Download and set-up the LSC package.
Follow the tutorial to see how LSC works on some example data.
Read the manual if anything is unclear.
You're ready, Happy LSCing!

Latest publication

Kin Fai Au, Jason Underwood, Lawrence Lee and Wing Hung Wong
Improving PacBio Long Read Accuracy by Short Read Alignment [Manuscript]
PLoS ONE 2012. 7(10): e46679. doi:10.1371/journal.pone.0046679

Address of the bookmark: https://www.healthcare.uiowa.edu/labs/au/LSC/

Savitribai Phule Pune University Recruitment for 04 JRF Post in April 2015

Mon, 27 Apr 2015 20:28:59 -0500

Savitribai Phule Pune University announced application for recruitment to the post of Junior Research Fellow. The candidates for the post can apply through prescribed format before 10 May 2015.
Description:

Important Date & Details

Closing Date for Registration: 10 May 2015

Details of Post

Name of Post: Junior Research Fellow- 04 Posts

Pay Scale: Rs. 12,000 or 16,00+ HRA Post Graduate degree with NET (16,000+HRA) Post Graduate Degree (12,000+HRA)

Eligibility Criteria: M.Sc. in Microbiology/Marine Microbiology/ Marine Biotechnology/Biotechnology/Bioinformatics/Zoology or equivalent degree with minimum 60% marks or equivalent grade

Age Limit- Not more than 28 years

Organisation Name: Savitribai Phule Pune University
Eligibility for the post:

Selection Procedure: The selection procedure is through personal interview. No TA/DA will be paid for appearing in the interview.

How to Apply: The candidates may send their application along with CV to the Head Department of Zoology, Savitribai Phule University on or before 10 May 2015.

LoRMA: A tool for correcting sequencing errors in long reads

Abhimanyu Singh — Thu, 06 Sep 2018 16:21:01 -0500

An error correction method that uses long reads only. The method consists of two phases: first, we use an iterative alignment-free correction method based on de Bruijn graphs with increasing length of k-mers, and second, the corrected reads are further polished using long-distance dependencies that are found using multiple alignments. According to our experiments, the proposed method is the most accurate one relying on long reads only for read sets with high coverage. Furthermore, when the coverage of the read set is at least 75×, the throughput of the new method is at least 20% higher.

conda install -c atgc-montpellier lorma

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

ClipCrop: a tool for detecting structural variations with single-base resolution using soft-clipping information

Rahul Nayak — Thu, 04 Oct 2018 16:39:28 -0500

This is a tool for detecting structural variations using soft-clipping information From SAM files.

https://github.com/shinout/clipcrop

Address of the bookmark: https://github.com/shinout/clipcrop