Frequently used bioinformatics tools for viral genome analysis !
IVA: accurate de novo assembly of RNA virus genomes. Hunt M, Gall A, Ong SH, Brener J, Ferns B, Goulder P, Nastouli E, Keane JA, Kellam P, Otto TD. Bioinformatics. 201...1062 days ago
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Genome Assembly Tools and Software - PART2 !!
...option to estimate insert size distributions from data. VGA v1 – Viral Genome AssemblerVGA is a method for accurate assembly of a heterogeneous viral population consisting of indi...2700 days ago
Bioinformatics in Africa: Part7 - Tunisia
...on infectious diseases, and R/D on vaccines. Research programs are mainly oriented towards local health problems such as leishmaniais, viral hepatitis, and scorpion venom...1198 days ago
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Genome Assembly Tools and Software - PART1 !!
...cifically for scaffolding diploid genomes. HaploClique 0.1 – Viral Quasispecies Assembly from Pa...ploClique is a computational approach to reconstruct the structure of a viral quasispecies from next-genera...2700 days ago
100K Foodborne Pathogen Genome Project
...public database at the National Center for Biotechnology Information. 100K Genome Project, aims to sequence the genomes of 100,000 bacterial and viral genomes. http://100kgenome.v...3938 days ago
320000 viruses in mammals yet to sequenced in future!!!
...o look at millions of unknown viruses at genomic level and understand the mechanism. According to available data, close to 70 per cent of emerging viral diseases such as HIV/AIDS, We...3911 days ago
2 positions on the evolutionary analysis of biological sequences in Montpellier - France
...European VIROGENESIS project (http://www.kuleuven.be/english/research/EU/p/horizon2020/sc/sc1/Virogenesis), concerns the evolutionary analysis of viral sequences. Topics include --...3157 days ago
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Retrovirus Replication 3D Animation
...y that is sufficient in detail for upper level coursework and possibly graduate coursework. * Modes of action for some anti-viral drugs are also described. NOTE: The viral genome in the form of DNA sta...3859 days ago
Download the genome from NCBI using bash script/command
...'s|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|\1\2/\2_genomic.fna.gz|' > genomic_file_invertebrate # -for viral curl 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/viral/assembly_summary.txt' | awk '...2547 days ago
Download the gff files from NCBI using bash script/command
...'s|(ftp://ftp.ncbi.nlm.nih.gov/genomes/all/.+/)(GCF_.+)|\1\2/\2_genomic.gff.gz|' > genomic_file_invertebrate # -for viral curl 'ftp://ftp.ncbi.nlm.nih.gov/genomes/refseq/viral/assembly_summary.txt' | awk '...2538 days ago
Tags: VICUNA, software, tool, enables, consensus, assembly, ultra-deep, sequence, diverse, viral, heterogeneous, populations
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LoReTTA, a user-friendly tool for assembling viral genomes from PacBio sequence data
LoReTTA (Long Read Template-Targeted Assembler), a tool designed for performing de novo assembly of long reads generated from viral genomes on the PacBio platform. LoReTTA exploits a reference genome to guide the assembly process, an approach that has been successful with short reads. https://ac...Tags: LoReTTA, user-friendly, tool, assembly, viral, genomes, PacBio, sequence, data
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Comment on "Calling variants in non-diploid systems"
...s where the number of samples is not known. This is the exact scenario we have here: in our sample we have multiple mitochondrial (or bacterial or viral) genomes, but we do not know...1058 days ago