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nQuire: A statistical framework for ploidy estimation using NGS short-read data
By Jit 2123 days agogithub.com - nQuire implements a set of commands to estimate ploidy level of individuals from species, where recent polyploidization occurred and intraspecific ploidy variation is observed. Specifically, nQuire uses next-generation sequencing data to distinguish...LoFreq*: A sequence-quality aware, ultra-sensitive variant caller for NGS data
By BioStar 1740 days agocsb5.github.io - LoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or...McClintock: Meta-pipeline to identify transposable element insertions using next generation...
By BioStar 1489 days agogithub.com - an integrated bioinformatics pipeline for the detection of TE insertions in whole-genome shotgun data, called McClintock (https://github.com/bergmanlab/mcclintock), which automatically runs and standardizes output for multiple TE detection methods....Managing and Analyzing Next-Generation Sequence Data
By Rahul Agarwal 3850 days agowww.ploscompbiol.org - Centralized Bioinformatics Core Facilities provide shared resources for the computational and IT requirements of the investigators in their department or institution. As such, they must be able to effectively react to new types of experimental...How to sequence the human genome - Mark J. Kiel
By Rahul Nayak 3830 days agoView full lesson: http://ed.ted.com/lessons/how-to-sequence-the-human-genome-mark-j-kiel Your genome, every human's genome, consists of a unique DNA sequence of A's, T's, C's and G's that tell your cells how to operate. Thanks to technological...Scaffolding of a bacterial genome using MinION nanopore sequencing
By Rahul Agarwal 3427 days agowww.nature.com - Second generation sequencing has revolutionized genomic studies. However, most genomes contain repeated DNA elements that are longer than the read lengths achievable with typical sequencers, so the genomic order of several generated contigs cannot...Bioinformatics WalkIn at NII
ADVERTISEMENT OF WALK-IN-INTERVIEW NAME OF THE POST : Bioinformatician (Part time 3 days in a week) (One Position only) DURATION : One Year NAME OF THE PROJECT : Next generation sequencing facility EDUCATIONAL QUALIFICATIONS : At least a...
List of Bioinformatics Software Tools for Next Generation Sequencing
Last updated 3111 days ago by JitCommercial tools Strand NGS offers many different tools including alignment, RNA-Seq, DNA-Seq, ChIP-Seq, Small RNA-Seq, Genome Browser, visualizations, Biological Interpretation, etc. Supports workflows “one can import the sample data in...-
Genome Assembly Tools and Software - PART1 !!
Last updated 2888 days ago by JitThe genome assemblers generally take a file of short sequence reads and a file of quality-value as the input. Since the quality-value file for the high throughput short reads is usually highly memory-intensive, only a few assemblers, best suited for... Jvarkit : Java utilities for Bioinformatics
By Jit 2360 days agolindenb.github.io - Collection of Java tool kits for bioinformatics works: Jvarkit : Java utilities for Bioinformatics
