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IVA: accurate de novo assembly of RNA virus genomes
By Neel 1930 days agogithub.com - IVA (Iterative Virus Assembler) designed specifically for read pairs sequenced at highly variable depth from RNA virus samples. We tested IVA on datasets from 140 sequenced samples from human immunodeficiency virus-1 or influenza-virus-infected...ncbi-datasets-cli -- Quickstart: command line tools !
By Jit 1763 days ago Comments (1)www.ncbi.nlm.nih.gov - Install and use the NCBI Datasets command line tools The NCBI Datasets datasets command line tools are datasets and dataformat . Use datasets to download biological sequence data across all domains of life from...PLAR: Pipeline for lncRNA annotation from RNA-seq data
By Abhi 1732 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...Smudgeplot: Inference of ploidy and heterozygosity structure using whole genome sequencing data
By Neel 1683 days agogithub.com - This tool extracts heterozygous kmer pairs from kmer count databases and performs gymnastics with them. We are able to disentangle genome structure by comparing the sum of kmer pair coverages (CovA + CovB) to their relative coverage (CovB / (CovA +...Monkeypox virus isolate MPXV_USA_2022_MA001, complete genome
By Jit 1532 days agowww.ncbi.nlm.nih.gov - LOCUS ON563414 197205 bp DNA linear VRL 30-MAY-2022 DEFINITION Monkeypox virus isolate MPXV_USA_2022_MA001, complete genome. ACCESSION ON563414 VERSION ON563414.3 KEYWORDS . SOURCE Monkeypox virus...MitoHiFi: a python pipeline for mitochondrial genome assembly from PacBio high fidelity reads
By Abhi 1126 days agogithub.com - MitoHiFi v3.2 is a python pipeline distributed under MIT License ! MitoHiFi was first developed to assemble the mitogenomes for a wide range of species in the Darwin Tree of Life Project...quarTeT: a telomere-to-telomere toolkit for gap-free genome assembly and centromeric repeat...
By Abhi 849 days agowww.atcgn.com - quarTeT is a collection of tools for T2T genome assembly and basic analysis in automatic workflow.Task include: AssemblyMapper : reference-guided genome assembly GapFiller : long-reads based gap filling TeloExplorer : telomere...nf-core/mag v5: Advancing Genome-Resolved Metagenomics
By LEGE 23 days agoMetagenomics is rapidly moving beyond short-read sequencing. With the increasing adoption of long-read technologies, researchers can generate more contiguous assemblies—but converting these reads into reliable metagenome-assembled genomes (MAGs)...BIGRE Lab
The Laboratoire de Bioinformatique des Génomes et des Réseaux (Genome and Network Bioinformatics) is specialized in the conception, implementation, evaluation and application of bioinformatics approaches for the analysis of genome, transcriptome,...Sorghum genome Sequenced!!
By Jit 4782 days agoRecently published paper in Nature communication provide an insight on Africa’s indigenous cereal crop sorghum.
