BOL

CoViD Selection analysis http://virological.org/t/selection-analysis-of-gisaid-sars-cov-2-data/448

UK resource in CoViD19 http://cov-glue.cvr.gla.ac.uk/#/home https://macman123.shinyapps.io/ugi-scov2-alignment-screen/

Molecular informatics journal is also a good alternative for bioinformatics tools publication https://onlinelibrary.wiley.com/toc/18681751/2020/39/4

SyRI is a comprehensive tool for predicting genomic differences between related genomes using whole-genome assemblies (WGA). The assemblies are aligned using whole-genome alignment tools, and these alignments are then used as input to SyRI. SyRI...

NucDiff locates and categorizes differences between two closely related nucleotide sequences. It is able to deal with very fragmented genomes, structural rearrangements and various local differences. These features make NucDiff to be perfectly...

HASLR, a hybrid assembler which uses both second and third generation sequencing reads to efficiently generate accurate genome assemblies. Our experiments show that HASLR is not only the fastest assembler but also the one with the lowest number of...

*****WARNING: Query v300043428L4C001R0481272249 is marked as paired, but its mate does not occur next to it in your BAM file.  Skipping.

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...

a) bowtie2 mapping against host sequence Host example: human genome hg19 (download bowtie2 hg19 index)# 1) create bowtie2 index database (host_DB) from host reference genomebowtie2-build host_genome.fna host_DB# 2) bowtie2...

How to filter out host reads from paired-end fastq files?

Max 3' match

FlexiDot is a cross-platform dotplot suite generating high quality self, pairwise and all-against-all visualizations. To improve dotplot suitability for comparison of consensus and error-prone sequences, FlexiDot harbors routines for strict and...

Deeply conserved synteny resolves early events in vertebrate evolution https://www.nature.com/articles/s41559-020-1156-z #Synteny #Evolution #Vertebrate

Centre for Development of Advanced Computing (C-DAC) under the aegis of the National Supercomputing Mission (NSM), a Ministry of Electronics & Information Technology (MeitY) and Department of Science & Technology (DST) initiative, in...

Visualize genome in terminal https://asciigenome.readthedocs.io/en/latest/usage.html#quick-start #genome #visualisation

WEGO (Web Gene Ontology Annotation Plot) is a simple but useful tool for visualizing, comparing and plotting GO (Gene Ontology) annotation results. As the GO vocabulary became more and more popular, WEGO was widely adopted and used in many...

Aerosol and Surface Stability of SARS-CoV-2 as Compared with SARS-CoV-1 https://www.nejm.org/doi/pdf/10.1056/NEJMc2004973 #corona #CoVID

CSAR-web is a web-based tool that allows the users to efficiently and accurately scaffold (i.e. order and orient) the contigs of a target draft genome based on a complete or incomplete reference genome from a related organism.  CSAR-web can...