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assemblytics: delta file to analyze alignments of an assembly to another assembly or a reference...
By Jit 2332 days agohttp://assemblytics.com/ - Download and install MUMmer Align your assembly to a reference genome using nucmer (from MUMmer package) $ nucmer -maxmatch -l 100 -c 500 REFERENCE.fa ASSEMBLY.fa -prefix OUT Consult the MUMmer manual if you encounter problems Optional: Gzip...HaploMerger2: rebuilding both haploid sub-assemblies from high-heterozygosity diploid genome...
By BioStar 2227 days agogithub.com - HM2 can process any diploid assemblies, but it is especially suitable for diploid assemblies with high heterozygosity (≥3%), which can be difficult for other tools. This pipeline also implements flexible and sensitive assembly error detection, a...DECIPHER
By Anjana 2954 days agodecipher.cee.wisc.edu - DECIPHER is a software toolset that can be used to maintain, analyze, and decipher large amounts of DNA sequence data. To install DECIPHER, see the Downloads page. To begin using DECIPHER read the "Getting Started DECIPHERing" tutorial. Refer to the...
Evaluation of genome assembly software based on long reads
By BioStar 2100 days agoTGS technologies have been used to produce highly accurate de novo assemblies of hundreds of microbial genomes and highly contiguous reconstructions of many dozens of plant and animal genomes, enabling new insights into evolution and sequence...GMASS: a novel measure for genomeassembly structural similarity
By Abhimanyu Singh 2028 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...Beagle
By Jit 2927 days agofaculty.washington.edu - Beagle is a software package that performs genotype calling, genotype phasing, imputation of ungenotyped markers, and identity-by-descent segment detection. Beagle version 4.1 has a more accurate genotype phasing algorithm and a very fast and...SvABA: Structural variation and indel detection by local assembly
By Jit 1697 days agogithub.com - SvABA is a method for detecting structural variants in sequencing data using genome-wide local assembly. Under the hood, SvABA uses a custom implementation of SGA (String Graph Assembler) by Jared Simpson, and BWA-MEM by Heng Li....ART: Set of Simulation Tools
By Jit 2920 days agowww.niehs.nih.gov - ART is a set of simulation tools to generate synthetic next-generation sequencing reads. ART simulates sequencing reads by mimicking real sequencing process with empirical error models or quality profiles summarized from large recalibrated...RefKA: A fast and efficient long-read genome assembly approach for large and complex genomes
By Rahul Nayak 1646 days agogithub.com - RefKA, a reference-based approach for long read genome assembly. This approach relies on breaking up a closely related reference genome into bins, aligning k-mers unique to each bin with PacBio reads, and then assembling each bin in parallel...R Graphs !!
By Jit 2919 days ago Comments (1)rgraphgallery.blogspot.be - The blog is a collection of script examples with example data and output plots. R produce excellent quality graphs for data analysis, science and business presentation, publications and other purposes. Self-help codes and examples are provided....
