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RefKA: A fast and efficient long-read genome assembly approach for large and complex genomes
By Rahul Nayak 1657 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...merqury: Evaluate genome assemblies with k-mers
By Jit 1593 days agogithub.com - Often, genome assembly projects have illumina whole genome sequencing reads available for the assembled individual. The k-mer spectrum of this read set can be used for independently evaluating assembly quality without the need of a high quality...HapSolo: An optimization approach for removing secondary haplotigs during diploid genome assembly...
By Jit 1478 days agogithub.com - Despite marked recent improvements in long-read sequencing technology, the assembly of diploid genomes remains a difficult task. A major obstacle is distinguishing between alternative contigs that represent highly heterozygous regions. If primary...HapSolo: An optimization approach for removing secondary haplotigs during diploid genome assembly...
By Jit 1284 days agogithub.com - HapSolo, that identifies secondary contigs and defines a primary assembly based on multiple pairwise contig alignment metrics. HapSolo evaluates candidate primary assemblies using BUSCO scores and then distinguishes among candidate assemblies using...Josefa González Lab
Lab focus on understanding how organisms adapt to their environments. They combine omics approaches with detailed molecular and phenotypic analyses to get a comprehensive picture of adaptation. Our aim at being internationally recognized as a...Illumina based assembly pipeline steps !
By Surabhi Chaudhary 1069 days agoGenome assembly pipeline !chromeister: An ultra fast, heuristic approach to detect conserved signals in extremely large...
By Jit 1014 days agogithub.com - chromeister: An ultra fast, heuristic approach to detect conserved signals in extremely large pairwise genome comparisons. USAGE: -query: sequence A in fasta format -db: sequence B in fasta format -out: output matrix -kmer Integer: k>1...Bioinfo Lab
The Institute of Bioinformatics conducts internationally renowned research and provides profound education in bioinformatics. Its research focuses on development and application of machine learning and statistical methods in biology and...genomenotebook
By Abhi 573 days agodbikard.github.io - https://dbikard.github.io/genomenotebook/ Install pip install genomenotebook How to use Create a simple genome browser with a search bar. The sequence appears when zooming in. import genomenotebook as gn g=gn.GenomeBrowser(genome_path,...PhyloHerb: A high‐throughput phylogenomic pipeline for processing genome skimming data
By Abhi 434 days agogithub.com - Phylogenomic Analysis Pipeline for Herbarium Specimens What is PhyloHerb: PhyloHerb is a wrapper program to process genome skimming data collected from plant materials. The outcomes include the plastid genome (plastome) assemblies,...
