BOL: Related items

GraphMap - A highly sensitive and accurate mapper for long, error-prone reads

Rahul Agarwal — Mon, 06 Jul 2015 08:46:53 -0500

GraphMap is a novel mapper targeted at aligning long, error-prone third-generation sequencing data.
It is designed to handle Oxford Nanopore MinION 1d and 2d reads with very high sensitivity and accuracy, and also presents a significant improvement over the state-of-the-art for PacBio read mappers.

GraphMap was also designed for ease-of-use: the default parameters can handle a wide range of read lengths and error profiles, including: Illumina, PacBio and Oxford Nanopore.
This is an especially important feature for technologies where the error rates and error profiles can vary widely across, or even within, sequencing runs.

http://biorxiv.org/content/early/2015/06/10/020719

Address of the bookmark: https://github.com/isovic/graphmap

CovCal: Coverage / Read Count Calculator

Jit — Wed, 15 Jun 2016 18:08:13 -0500

Coverage / Read Count Calculator

Calculate how much sequencing you need to hit a target depth of coverage (or vice versa).

Instructions: set the read length/configuration and genome size, then select what you want to calculate.

Written by Stephen Turner, based on the Lander-Waterman formula, inspired by a similar calculator written by James Hadfield. Coverage is calculated as C=LN/G and reads as N=CG/L where C = Coverage (X),L = Read length (bp), G = Haploid genome size (bp), and N = Number of reads. Source code on GitHub.

Address of the bookmark: http://apps.bioconnector.virginia.edu/covcalc/

SIMBA: a web tool for managing bacterial genome assembly generated by Ion PGM sequencing technology

Abhimanyu Singh — Tue, 23 May 2017 05:28:56 -0500

SIMBA, SImple Manager for Bacterial Assemblies, is a Web interface for managing assembly projects of bacterial genomes. SIMBA was created to assist bioinformaticians to assemble bacterial genomes sequenced with NextGeneration Sequencing (NGS) platforms quickly, easily and effectively. SIMBA also is open source tool, i.e., can be freely downloaded, shared and modified.

https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-016-1344-7

Address of the bookmark: http://ufmg-simba.sourceforge.net/

Jabba: Hybrid Error Correction for Long Sequencing Reads

Jit — Fri, 05 Jan 2018 03:58:14 -0600

Jabba is a hybrid error correction tool to correct third generation (PacBio / ONT) sequencing data, using second generation (Illumina) data.

Input

Jabba takes as input a concatenated de Bruijn graph and a set of sequences:

the de Bruijn graph should appear in fasta format with 1 entry per node, the meta information should be in the format:
>NODE
the set of sequences should be in fasta or fastq format. These sequences will be corrected (e.g. PacBio reads). The corrections will be written to a file Jabba fasta.
The output is a file in fasta format with corrections of the long reads, and additionally a file in the input format containing uncorrected reads.

https://github.com/biointec/jabba/wiki

https://almob.biomedcentral.com/articles/10.1186/s13015-016-0075-7

Address of the bookmark: https://github.com/biointec/jabba

Scientist Bioinformatics Positions

Thu, 30 Jan 2020 06:53:40 -0600

Bioinformatics-Multi_Omics_Integration

https://www.researchgate.net/job/939073_Senior_Scientist_Bioinformatics-Multi_Omics_Integration

Senior_Scientist_Bioinformatics-Transcriptomics_Analysis

https://www.researchgate.net/job/939075_Senior_Scientist_Bioinformatics-Transcriptomics_Analysis-Belgium_France_Switzerland_The_Netherlands

Senior Scientist Bioinformatics - Network Analytics

https://www.researchgate.net/job/939070_Senior_Scientist_Bioinformatics-Network_Analytics_Belgium_France_Switzerland_the_Netherlands

Team Leader Bioinformatics Data Sciences - Mechelen, Belgium

https://www.researchgate.net/job/938787_Team_Leader_Bioinformatics_Data_Sciences-Mechelen_Belgium

FiNGS: Filters for Next Generation Sequencing

Neel — Sat, 27 Feb 2021 01:18:35 -0600

Key features

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

Genetic Test in India

Rahul Agarwal — Sun, 11 Aug 2013 10:54:35 -0500

1.Xcode Life Sciences Pvt. Ltd.
6B, Eldorado,
112, Nungambakkam High Road,
Nungambakkam, Chennai 600034
Tamil Nadu, India

2.Mapmygenome™
Royal Demeure,HUDA Techno Enclave,
Plot No. 12/2, Sector-1 500 081
Madhapur,Hyderabad
AP, India

3. DNA Labs India

http://www.dnalabsindia.com/lab.php

4.MedGenome Labs Pvt Ltd
(Division of SciGenom Labs Pvt Ltd.)
Plot no: 43A,SDF, 3rd floor
A Block,CSEZ, Kakanad, Cochin
Kerala - 682037
Phone: 0484 - 2413399
Fax: 0484 - 2413398
Email: info@medgenome.com

5.Narayana Nethralaya

Narayana Hrudayalaya Campus
Narayana Health City
# 258/A, Bommasandra, Hosur Road,
Bangalore - 560 099 - INDIA.
TEL: +91-80-66660655-0658
FAX: +91-80-66660650
Mobile: 9902 821128 (Emergency Only)
e-mail: info@narayananethralaya.com

6.BioAxis DNA Research Centre Private Limited
13-51,Sri Lakshmi Nagar colony,
Besides Big Bazar, Near Kamineni Hospitals
GSI Post BandalGuda (L B Nagar) Hydeabad-500068
Andhra Pradesh (India).
Phone : +91-40-24034503/+91-9246338983

7.Gene Guiide

8th Floor, Embassy Towers, 7 Bungalows Rd, Versova, Andheri West, Mumbai-61
09167 117799
info@geneguiide.com

See more at: http://www.geneguiide.com

8.INDIAN BIOSCIENCES
Regd. Office:
G-2 (Ground Floor Rear), Kailash Colony, New Delhi - 110048, India.
Phone: +91 (0)11 29236088, Email: info@inbdna.com.

9.SRL Limited

GP-26, MARUTI INDUSTRIAL ESTATE,

UDYOG VIHAR,SECTOR-18,

GURGAON - 122015

Tel: 0124-3001243 / 0124-3001209

SRL Limited
VASANT VIHAR, 8, PALAM MARG,
NEW DELHI - 110057
Tel: 011 - 4229 5333

Website: http://www.srlworld.com
National Customer care number:
Call Toll Free : 1800-222-660/1800-102-8282
E-mail id: customercare@srl.in

10.Tata Memorial Centre,

Advanced Centre for Treatment, Research and Education in Cancer

Kharghar, Navi Mumbai - 410 210, INDIA.

Tel: +91-22-2740 5000

Fax: +91-22-2740 5085

E-mail: mail@actrec.gov.in

Illuminating next generation sequencing data with Go

Rahul Agarwal — Fri, 23 Aug 2013 07:13:33 -0500

Another good lecture for Illumina sequencing data analysis from

Dan Kortschak, Bioinformatics Group, School of Molecular and Biomedical Science ,The University of Adelaide

Address of the bookmark: http://talks.biogo.googlecode.com/git/illumination/illumination.pdf

Introduction of Epigenomics

Rahul Agarwal — Sun, 06 Oct 2013 04:59:30 -0500

Address of the bookmark: http://www.genome.gov/27532724

Your stress/depression came from ancestor

Rahul Agarwal — Sun, 04 May 2014 18:46:20 -0500

"A study published in Nature Neuroscience finds that stress in early life alters the production of small RNAs, called microRNAs, in the sperm of mice. The mice show depressive behaviours that persist in their progeny."

Source:

http://www.nature.com/news/sperm-rna-carries-marks-of-trauma-1.15049