BOL: Related items

Langya Virus Update !

Neel — Fri, 12 Aug 2022 05:31:10 -0500

https://www.ncbi.nlm.nih.gov/nuccore/OM101125,OM101126,OM101127,OM101128,OM101129,OM101130?

Zoonotic Henipavirus

https://pubmed.ncbi.nlm.nih.gov/35921459/

https://www.ncbi.nlm.nih.gov/nuccore/OM069646,,OM069567,OM069568,OM069569,OM069570,OM069571,OM069572,OM069573,OM069574,OM069575,OM069576,OM069577,OM069578,OM069579,OM069580,OM069581,OM069582,OM069583,OM069584,OM069585,OM069586,OM069587,OM069588,OM069589,OM069590,OM069591,OM069592,OM069593,OM069594,OM069595,OM069596,OM069597,OM069598,OM069599,OM069600,OM069601,OM069602,OM069603,OM069604,OM069605,OM069606,OM069607,OM069608,OM069609,OM069610,OM069611,OM069612,OM069613,OM069614,OM069615,OM069616,OM069617,OM069618,OM069619,OM069620,OM069621,OM069622,OM069623,OM069624,OM069625,OM069626,OM069627,OM069628,OM069629,OM069630,OM069631,OM069632,OM069633,OM069634,OM069635,OM069636,OM069637,OM069638,OM069639,OM069640,OM069641,OM069642,OM069643,OM069644,OM069645,OM069646

Sequencing Solutions to World Health

Rahul Agarwal — Thu, 29 Aug 2013 15:05:35 -0500

"New technology that quickly, easily and economically reveals the genomes of viruses and pathogens transforms public health and medicine."

Source: Life technologies

Address of the bookmark: http://www.lifetechnologies.com/global/en/home/communities-social/blog/blogs/sequencing-solutions-to-world-health.html?cid=social_blogseries_20130829_11098264

Frequently used bioinformatics tools for viral genome analysis !

Neel — Wed, 23 Jun 2021 07:40:41 -0500

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. 2015 Jul 15;31(14):2374-6. doi: 10.1093/bioinformatics/btv120. Epub 2015 Feb 28.

Adapter sequences:
Optimal enzymes for amplifying sequencing libraries.
Quail, M. a et al. Nat. Methods 9, 10-1 (2012).

GAGE:
GAGE: A critical evaluation of genome assemblies and assembly algorithms.
Salzberg, S. L. et al. Genome Res. 22, 557-67 (2012).

KMC:
Disk-based k-mer counting on a PC.
Deorowicz, S., Debudaj-Grabysz, A. & Grabowski, S. BMC Bioinformatics 14, 160 (2013).

Kraken:
Kraken: ultrafast metagenomic sequence classification using exact alignments.
Wood, D. E. & Salzberg, S. L. Genome Biol. 15, R46 (2014).

MUMmer:
Versatile and open software for comparing large genomes.
Kurtz, S. et al. Genome Biol. 5, R12 (2004).

R:
R: A language and environment for statistical computing.
R Core Team (2013). R Foundation for Statistical Computing, Vienna, Austria. URL http://www.R-project.org/.

RATT:
RATT: Rapid Annotation Transfer Tool.
Otto, T. D., Dillon, G. P., Degrave, W. S. & Berriman, M. Nucleic Acids Res. 39, e57 (2011).

SAMtools:
The Sequence Alignment/Map format and SAMtools.
Li, H. et al. Bioinformatics 25, 2078-9 (2009).

Trimmomatic:
Trimmomatic: A flexible trimmer for Illumina Sequence Data.
Bolger, A. M., Lohse, M. & Usadel, B. Bioinformatics 1-7 (2014).

Monkeypox virus isolate MPXV_USA_2022_MA001, complete genome

Jit — Tue, 26 Jul 2022 06:21:07 -0500

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 (monkeypox)
  ORGANISM  Monkeypox virus
            Viruses; Varidnaviria; Bamfordvirae; Nucleocytoviricota;
            Pokkesviricetes; Chitovirales; Poxviridae; Chordopoxvirinae;
            Orthopoxvirus.

Address of the bookmark: https://www.ncbi.nlm.nih.gov/nuccore/ON563414