• Filters SNVs from any variant caller to remove false positives
• Calculates metrics based on BAM files and provides filtering not possible with other tools
• Fully user-configurable filtering (including which filters to use and their thresholds)
• Option to use filters identical to ICGC recommendations

FiNGS provides researchers with a tool to reproducibly filter somatic variants that is simple to both deploy and use, with filters and thresholds that are fully configurable by the user. It ingests and emits standard variant call format (VCF) files and will slot into existing sequencing pipelines. It allows users to develop and implement their own filtering strategies and simple sharing of these with others.

FiNGS reliably improves upon the precision of default variant caller outputs and performs better than other tools designed for the same task.

Address of the bookmark: https://github.com/cpwardell/FiNGS

The developers and expert trainers are the authors of several popular R packages, including ggplot2, plyr, lubridate, and others.

More at http://www.rstudio.com/

http://www.rstudio.com/products/RStudio/

Address of the bookmark: http://www.rstudio.com/

More at https://nikbaya.github.io/brava_browser/#/

Address of the bookmark: https://nikbaya.github.io/brava_browser/#/

Handle sequence locations for bioinformatics http://www.ingolia-lab.org/seqloc-tutorial.html

Address of the bookmark: http://www.stackage.org/snapshot/nightly-2014-12-28/package/seqloc-0.6

Quickstart

http://nanopolish.readthedocs.io/en/latest/quickstart_consensus.html

Algorithms

http://simpsonlab.github.io/2017/06/30/nanopolish-v0.7.0/

Address of the bookmark: https://github.com/jts/nanopolish

Website: www.actrec.gov.in; Ph: 27405000

No. ACTREC/Advt./ 66 /2014 23rd December, 2014
Research Associate

International Cancer Genome Consortium (ICGC) - India Project (IRB Project No. 3 A/c. No. 2408)

Dr. Rajiv Sarin

Duration of the Project: One year Extendable up to Three years.

Consolidated Salary: Rs. 42,000/- p.m.

Application last date: 8th January, 2015.

Interview Date & Time: 21st January, 2015, at 11.00 a.m.

Venue: Conference Room, 3rd floor, Khanolkar Shodhika, ACTREC.

Essential Qualifications and Experience:

Ph.D (any branch of Life Sciences)

The candidate must have at least one year experience after Ph.D., preferably in Genomics and Molecular Biology.

Candidates fulfilling these requirements should pre register themselves by sending their application in the prescribed format with recent CV and contact details of 2 referees by e-mail to icgc@actrec.gov.in latest 8th January, 2015 by 10.00 a.m.

Candidates shortlisted for the interview will be intimated by email on or before 9th January, 2015.

The interviews would be held on 21st January 2015 and will be only for the pre registered candidates who have been shortlisted.
No T.A./D.A. will be admissible for attending the interview.

At the time of Interview the candidate should bring original certificates along with CV with contact details of 2 referees and submit the photocopies (attested) of the certificates, with a recent passport size photograph.

Advertisement: www.actrec.gov.in/data%20files/2014/Walk-in-Research-Fellow-26-12-14.doc

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/

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

For example ... contig-stats.pl is a Perl script that will automatically describe features of a sequence assembly.

http://milkweedgenome.org/?q=scripts

Address of the bookmark: http://milkweedgenome.org/?q=scripts

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

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