<![CDATA[BOL: Related items]]> https://bioinformaticsonline.com/related/37536?offset=90 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/41146/lofreq-a-sequence-quality-aware-ultra-sensitive-variant-caller-for-ngs-data Tue, 18 Feb 2020 03:24:22 -0600 https://bioinformaticsonline.com/bookmarks/view/41146/lofreq-a-sequence-quality-aware-ultra-sensitive-variant-caller-for-ngs-data <![CDATA[LoFreq*: A sequence-quality aware, ultra-sensitive variant caller for NGS data]]> LoFreq* (i.e. LoFreq version 2) is a fast and sensitive variant-caller for inferring SNVs and indels from next-generation sequencing data. It makes full use of base-call qualities and other sources of errors inherent in sequencing (e.g. mapping or base/indel alignment uncertainty), which are usually ignored by other methods or only used for filtering.

https://github.com/CSB5/lofreq

http://csb5.github.io/lofreq/installation/

https://github.com/CSB5/lofreq/tree/master/dist

Address of the bookmark: http://csb5.github.io/lofreq/

]]> BioStar 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

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

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