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VG: variation graph data structures, interchange formats, alignment, genotyping, and variant...
By Jit 2447 days agogithub.com - Variation graphs provide a succinct encoding of the sequences of many genomes. A variation graph (in particular as implemented in vg) is composed of: nodes, which are labeled by sequences and ids edges, which connect two nodes via either of...Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation
By Neel 1650 days agogithub.com - Merfin, a k-mer based variant-filtering algorithm for improved accuracy in genotyping and genome assembly polishing. Merfin evaluates each variant based on the expected k-mer multiplicity in the reads, independently of the quality of the...NextSV: a meta-caller for structural variants from low-coverage long-read sequencing data
By Jit 2986 days agogithub.com - NextSV, a meta SV caller and a computational pipeline to perform SV calling from low coverage long-read sequencing data. NextSV integrates three aligners and three SV callers and generates two integrated call sets (sensitive/stringent) for different...GMASS: a novel measure for genomeassembly structural similarity
By Abhimanyu Singh 2735 days agobioinfo.konkuk.ac.kr - The GMASS score is a novel measure for representing structural similarity between two assemblies. It will contribute to the understanding of assembly output and developing de novo...PRISM
By Jit 3590 days agocompbio.cs.toronto.edu - PRISM is a software for split read (reads which span across a structrual variant -- SV ) mapping and SV calling from the mapping result. PRISM is able to detect small insertions and abitrary size deletions, inversions and tandom duplications with...Recombination detection tool
By Jit 3903 days ago Comments (2)github.com - A program to detect recombination hotspots using population genetic data. More at https://github.com/auton1/LDhotRASTtk : algorithm for building custom annotation pipelines and annotating batches of genomes
By Abhi 3818 days agohttp://rast.nmpdr.org/ - The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes...MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping
By Neel 3794 days agojournals.plos.org - MOSAIK is a stable, sensitive and open-source program for mapping second and third-generation sequencing reads to a reference genome. Uniquely among current mapping tools, MOSAIK can align reads generated by all the major sequencing technologies,...GAEMR
By Jit 3770 days agowww.broadinstitute.org - The Genome Assembly Evaluation Metrics and Reporting (GAEMR) package is an assembly analysis framework composed a number of integrated modules. These modules can be executed as a single program to generate a complete...Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm)
By Abhimanyu Singh 3572 days agohttp://prodigal.ornl.gov/ - Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee. Key features of Prodigal...
