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HASLR: a hybrid assembler which uses both second and third generation sequencing reads
By BioStar 1663 days agogithub.com - HASLR, a hybrid assembler which uses both second and third generation sequencing reads to efficiently generate accurate genome assemblies. Our experiments show that HASLR is not only the fastest assembler but also the one with the lowest number of...Recombination detection tool
By Jit 3216 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 3131 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 3107 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 3083 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...HivePlot
By Jit 2836 days agohttp://www.hiveplot.com/ - The hive plot is a rational visualization method for drawing networks. Nodes are mapped to and positioned on radially distributed linear axes — this mapping is based on network structural properties. Edges are drawn as curved links....HGT-Finder: A New Tool for Horizontal Gene Transfer Finding and Application to Aspergillus genomes
By Jit 2501 days agowww.ncbi.nlm.nih.gov - HGT-Finder: (i) can be used for HGT detection in both prokaryotes and eukaryotes, (ii) can report a statistical P value for each gene to indicate how likely it is to be horizontally transferred, and (iii) is fully automated (requires...MGERT: Mobile Genetic Elements Retrieving Tool
By Neel 2015 days agogithub.com - MGERT is a computational pipeline for easy retrieving of MGE's coding sequences of a particular family from genome assemblies. MGERT utilizes several established bioinformatic tools combined into single pipeline which hides different...R Package for PCA Analysis
By LEGE 242 days agorpubs.com - An R package for performing principal component analysis (PCA) of genomics data. The package performs PCA, generates the publication-ready plots, and identifies population-specific outlier individuals. The package can be accessed on...DAVI: Deep learning-based tool for alignment and single nucleotide variant identification
By Jit 1347 days ago Comments (1)github.com - DAVI consists of models for both global and local alignment and for variant calling. We have evaluated the performance of DAVI against existing state-of-the-art tool sets and found that its accuracy and performance is comparable to existing tools...
