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Understanding HiFi Reads !
By Rahul Nayak 974 days agopacb.com - While little public data is available for either of the new synthetic long read approaches, Illumina showed an example comparison earlier this year at the Festival of Genomics & Biodata conference (FoG 2022). In the IGV screenshot...COSMIC
By Jit 2974 days agocancer.sanger.ac.uk - The accurate description and annotation of structural variants can be complex. This is due to the different resolution that variants are reported from traditional cytogenetic coordinates down to the actual base pair positions....GRIDSS: the Genomic Rearrangement IDentification Software Suite
By Rahul Nayak 1650 days agogithub.com - GRIDSS is a module software suite containing tools useful for the detection of genomic rearrangements. GRIDSS includes a genome-wide break-end assembler, as well as a structural variation caller for Illumina sequencing data. GRIDSS calls variants...Tree illustrating the lack of interchromosomal rearrangement of the microchromosomes.
By BioJoker 2189 days agoTree illustrating the lack of interchromosomal rearrangement of the microchromosomes. No interchromosomal microchromosome fusions from the avian ancestor unless otherwise stated (macrochromosomal fusions not listed). The overall pattern of...Cactus: a reference-free whole-genome multiple alignment program
By Jit 1929 days agogithub.com - Cactus is a reference-free whole-genome multiple alignment program. The principal algorithms are described here: https://doi.org/10.1101/gr.123356.111 Cactus uses substantial resources. For primate-sized genomes (3 gigabases each), you should...BioGPS
By Anjana 3106 days agobiogps.org - A free extensible and customizable gene annotation portal, a complete resource for learning about gene and protein function. http://biogps.org/#goto=welcomeJPred4: A Protein Secondary Structure Prediction Server
By Poonam Mahapatra 2520 days agowww.compbio.dundee.ac.uk - JPred4 (http://www.compbio.dundee.ac.uk/jpred4) is the latest version of the popular JPred protein secondary structure prediction server which provides predictions by the JNet algorithm, one of the most accurate methods for secondary structure...GenomeThreader: Gene Prediction Software
By Neel 2242 days agogenomethreader.org - GenomeThreader is a software tool to compute gene structure predictions. The gene structure predictions are calculated using a similarity-based approach where additional cDNA/EST and/or protein sequences are used to predict gene structures via...GLEAN: an unsupervised learning system to integrate disparate sources of gene structure evidence
By Poonam Mahapatra 2365 days agosourceforge.net - GLEAN is an unsupervised learning system to integrate disparate sources of gene structure evidence (gene model predictions, EST/protein genomic sequence alignments, SAGE/peptide tags, etc) to produce a consensus gene prediction, without prior...miniasm: very fast OLC-based de novo assembler for noisy long reads
By Jit 2552 days agogithub.com - Miniasm is a very fast OLC-based de novo assembler for noisy long reads. It takes all-vs-all read self-mappings (typically by minimap) as input and outputs an assembly graph in the GFA format. Different from mainstream...
