<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/37993?offset=470 https://bioinformaticsonline.com/blog/view/43607/classification-of-sars-cov2-variant Fri, 26 Nov 2021 12:53:12 -0600 https://bioinformaticsonline.com/blog/view/43607/classification-of-sars-cov2-variant <![CDATA[Classification of SARS-CoV2 Variant !]]> The scientists established some guidelines for determining whether a variant is a legitimate branch of an existing lineage:

The variant should be transmitted from its original location to another "geographically distinct population"—say, another country or a province of a large and populous country.
It should differ from its ancestor by at least one nucleotide.
At least 95% of its genetic code should have been sequenced at least five times from different samples.

]]> Jit https://bioinformaticsonline.com/bookmarks/view/38004/vcfr-a-package-to-manipulate-and-visualize-vcf-data-in-r Thu, 25 Oct 2018 09:05:59 -0500 https://bioinformaticsonline.com/bookmarks/view/38004/vcfr-a-package-to-manipulate-and-visualize-vcf-data-in-r <![CDATA[vcfR: a package to manipulate and visualize VCF data in R]]> VcfR is an R package intended to allow easy manipulation and visualization of variant call format (VCF) data. Functions are provided to rapidly read from and write to VCF files. Once VCF data is read into R a parser function extracts matrices from the VCF data for use with typical R functions. This information can then be used for quality control or other purposes. Additional functions provide visualization of genomic data. Once processing is complete data may be written to a VCF file or converted into other popular R objects (e.g., genlight, DNAbin). VcfR provides a link between VCF data and the R environment connecting familiar software with genomic data.

Address of the bookmark: https://github.com/knausb/vcfR

]]> Jit https://bioinformaticsonline.com/bookmarks/view/43850/merfin-improved-variant-filtering-assembly-evaluation-and-polishing-via-k-mer-validation Sun, 03 Apr 2022 20:35:19 -0500 https://bioinformaticsonline.com/bookmarks/view/43850/merfin-improved-variant-filtering-assembly-evaluation-and-polishing-via-k-mer-validation <![CDATA[Merfin: improved variant filtering, assembly evaluation and polishing via k-mer validation]]> Merfin, a k-mer based variant-filtering algorithm for improved accuracy in genotyping and genome assembly polishing. Merfin evaluates each variant based on the expected k-mer multiplicity in the reads, independently of the quality of the read alignment and variant caller’s internal score. Merfin increased the precision of genotyped calls in several benchmarks, improved consensus accuracy and reduced frameshift errors when applied to human and nonhuman assemblies built from Pacific Biosciences HiFi and continuous long reads or Oxford Nanopore reads, including the first complete human genome. Moreover, we introduce assembly quality and completeness metrics that account for the expected genomic copy numbers.

More at https://www.nature.com/articles/s41592-022-01445-y

image

Address of the bookmark: https://github.com/arangrhie/merfin

]]> Neel