Abhimanyu Singh
A bioinformatics beginner
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IVA: accurate de novo assembly of RNA virus genomes
By Neel 1248 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...GenomeTools: The versatile open source genome analysis software
By Neel 1024 days agohttp://genometools.org/ - The GenomeTools genome analysis system is a free collection of bioinformatics tools (in the realm of genome informatics) combined into a single binary named gt. It is based on a C library named...Refseq viraal genome sequences !
By Jit 1077 days agoftp.ncbi.nlm.nih.gov - List of all viruses on NCBI https://ftp.ncbi.nlm.nih.gov/refseq/release/viral/
Short-read assembly using Spades !
Last updated 1026 days ago by Abhimanyu Singh Comments (2)If we only had Illumina reads, we could also assemble these using the tool Spades. You can try this here, or try it later on your own data. Get data We will use the same Illumina data as we used above: illumina_R1.fastq.gz: the Illumina...Smudgeplot: Inference of ploidy and heterozygosity structure using whole genome sequencing data
By Neel 1001 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 850 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 444 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 167 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...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 4100 days agoRecently published paper in Nature communication provide an insight on Africa’s indigenous cereal crop sorghum.
