Jit
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RefKA: A fast and efficient long-read genome assembly approach for large and complex genomes
By Rahul Nayak 2137 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 2073 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 1958 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...InfoGenomeR: Integrative reconstruction of cancer genome karyotypes
By Jit 1768 days agogithub.com - InfoGenomeR is the Integrative Framework for Genome Reconstruction that uses a breakpoint graph to model the connectivity among genomic segments at the genome-wide scale. InfoGenomeR integrates cancer purity and ploidy, total CNAs, allele-specific...Understanding kmer !
By BioStar 1662 days agobioinfologics.github.io - What is a k-mer anyway? A k-mer is just a sequence of k characters in a string (or nucleotides in a DNA sequence). Now, it is important to remember that to get all k-mers from a sequence you need to get...PLAR: Pipeline for lncRNA annotation from RNA-seq data
By Abhi 1520 days agowww.weizmann.ac.il - Due to several requests, we are releasing an assingment of orthologs, determined using the same methods used in Hezroni et al. (BLAST, Whole Genome Alignment (WGA), and synteny). One is comparing human GENCODE genes (from GENCODE v30) to lncRNAs...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 1052 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 914 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,...Genetic basis of tail-loss evolution
By LEGE 368 days agoThe study suggests that a specific genetic mutation, involving the insertion of an Alu element (a type of transposable DNA sequence), played a critical role in the evolutionary transition from tailed primates to tailless hominoids.
