Abhimanyu Singh
A bioinformatics beginner
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GMcloser: closing gaps in assemblies accurately with a likelihood-based selection of contig or...
By Shruti Paniwala 2359 days agoacademic.oup.com - GMcloser uses likelihood-based classifiers calculated from the alignment statistics between scaffolds, contigs and paired-end reads to correctly assign contigs or long reads to gap regions of scaffolds, thereby achieving accurate and efficient gap...GFinisher: a new strategy to refine and finish bacterial genome assemblies
By Jit 2313 days agogfinisher.sourceforge.net - GFinisher is an application tools for refinement and finalization of prokaryotic genomes assemblies using the bias of GC Skew to identify assembly errors and organizes the contigs/scaffolds with genomes references. java -Xms2G -Xmx4G -jar...NovoGraph: building whole genome graphs from long-read-based de novo assemblies
By Jit 2201 days agogithub.com - NovoGraph: building whole genome graphs from long-read-based de novo assemblies An algorithmically novel approach to construct a genome graph representation of long-read-based de novo sequence assemblies. We then provide a proof of...Integrative Meta-Assembly Pipeline (IMAP): Chromosome-level genome assembler combining multiple de...
By Jit 1912 days agojournals.plos.org - Chromosome-level genome assembler combining multiple de novo assemblies https://github.com/jkimlab/IMAPLiftoff: an accurate tool that maps annotations in GFF or GTF between assemblies
By Jit 1608 days agogithub.com - Liftoff, an accurate tool that maps annotations in GFF or GTF between assemblies of the same, or closely-related species. Unlike current coordinate lift-over tools which require a pre-generated “chain” file as input, Liftoff is a...GenomeQC: a quality assessment tool for genome assemblies and gene structure annotations
By Neel 921 days agogithub.com - The GenomeQC web application is implemented in R/Shiny version 1.5.9 and Python 3.6 and is freely available at https://genomeqc.maizegdb.org/ under the GPL license. All source code and a containerized version of the GenomeQC pipeline is...NGS course Medical Genomics, scheduled for 17-20 September 2013 in UZ Leuven (Belgium).
By Poonam Mahapatra 4122 days agoThe 4-day course is organized as a series of morning lectures and afternoon hands-on workshops.
Useful Publications and Websites for Deep Sequencing Data Analysis
Last updated 3983 days ago by Rahul NayakGlobal overview papers Next generation quantitative genetics in plants. Jiménez-Gómez, Frontiers in Plant Science 2:77, 2011 Full Text [equally relevant to animal and microbial systems] Sense from sequence reads: methods for...GABi
GABi Research The major researching fields defined as the GABi scope are described next: Sequence Analysis Protein Structure Prediction Comparative Genomics Functional Analysis of Residues on Protein Families Gene/Protein...Managing and Analyzing Next-Generation Sequence Data
By Rahul Agarwal 3852 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...
