Jit
Enthusiast computational biologist with business dream !!!
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assemblytics: delta file to analyze alignments of an assembly to another assembly or a reference...
By Jit 2384 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...sockeye
By Jit 2866 days agowww.bcgsc.ca - This sockeye software uses the Ensembl database project to import sequence and annotation information from several eukaryotic species. A user can additionally import their own custom sequence and annotation data. Individual annotation objects...HaploMerger2: rebuilding both haploid sub-assemblies from high-heterozygosity diploid genome...
By BioStar 2279 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...Referee: Genome assembly quality scores
By Jit 2241 days agogwct.github.io - Modern genome sequencing technologies provide a succint measure of quality at each position in every read, however all of this information is lost in the assembly process. Referee summarizes the quality information from the reads that map to a site...Software and Tools to detect structure variation with long reads !!
By Archana Malhotra 2840 days agoStructural variation caller tools using long reads
Evaluation of genome assembly software based on long reads
By BioStar 2152 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 2079 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...RefKA: A fast and efficient long-read genome assembly approach for large and complex genomes
By Rahul Nayak 1697 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...MitoZ: a toolkit for animal mitochondrial genome assembly, annotation and visualization
By Neel 1118 days agogithub.com - MitoZ, consisting of independent modules of de novo assembly, findMitoScaf (find Mitochondrial Scaffolds), annotation and visualization, that can generate mitogenome assembly together with annotation and visualization results from HTS raw...SciLifeLab tutorial for bioinformatics analysis !
By Jit 2442 days agoscilifelab.github.io - SciLifeLab is a national center for molecular biosciences with focus on health and environmental research. Courses Old courses (2012-2014) Metagenomics Workshop 2015 November - Uppsala2016 November - Uppsala2017 November - Uppsala Introduction...
