C
Christopher Pockrandt
Researcher at Johns Hopkins University
Publications - 19
Citations - 341
Christopher Pockrandt is an academic researcher from Johns Hopkins University. The author has contributed to research in topics: Approximate string matching & Biology. The author has an hindex of 6, co-authored 16 publications receiving 154 citations. Previous affiliations of Christopher Pockrandt include Max Planck Society & Free University of Berlin.
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Journal ArticleDOI
The SeqAn C++ template library for efficient sequence analysis: A resource for programmers
Knut Reinert,Temesgen Hailemariam Dadi,Marcel Ehrhardt,Hannes Hauswedell,Svenja Mehringer,René Rahn,Jongkyu Kim,Christopher Pockrandt,Jörg Winkler,Enrico Siragusa,Gianvito Urgese,David Weese +11 more
TL;DR: The SeqAn library of efficient data types and algorithms has matured considerably since its first publication 9 years ago and its status as an established resource for programmers in the field of sequence analysis is reviewed.
Journal ArticleDOI
GenMap: ultra-fast computation of genome mappability.
Christopher Pockrandt,Mai Alzamel,Mai Alzamel,Costas S. Iliopoulos,Knut Reinert,Knut Reinert +5 more
TL;DR: The mappability algorithm is extended, such that it can be computed across multiple genomes where a k-mer occurrence is only counted once per genome, which allows for the computation of marker sequences or finding candidates for probe design by identifying approximate k-mers that are unique to a genome or that are present in all genomes.
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Rapid detection of inter-clade recombination in SARS-CoV-2 with Bolotie.
TL;DR: Salzberg et al. as mentioned in this paper identified 225 anomalous SARS-CoV-2 genomes of likely recombinant origins out of the first 87,695 genomes to be released, several of which have persisted in the population.
Posted ContentDOI
Rapid detection of inter-clade recombination in SARS-CoV-2 with Bolotie
TL;DR: Bolotie is presented, an efficient method designed to detect recombination and reassortment events between clades of viral genomes that applied to a large collection of SARS-CoV-2 genomes and discovered hundreds of isolates that are likely of a recombinant origin.
Journal ArticleDOI
Metagenome analysis using the Kraken software suite
Jennifer Lu,Natalia Rincon,Derrick E. Wood,Florian P. Breitwieser,Christopher Pockrandt,Ben Langmead,Steven L. Salzberg,Martin Steinegger +7 more
TL;DR: The Kraken suite as mentioned in this paper is an end-to-end pipeline for the classification, quantification and visualization of metagenomic datasets, which is targeted to biologists and clinicians working in microbiome or metagenomics analysis who are familiar with the Unix command-line environment.