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Connor T. Skennerton
Researcher at California Institute of Technology
Publications - 23
Citations - 8915
Connor T. Skennerton is an academic researcher from California Institute of Technology. The author has contributed to research in topics: Population & Anaerobic oxidation of methane. The author has an hindex of 15, co-authored 21 publications receiving 4567 citations. Previous affiliations of Connor T. Skennerton include University of Queensland.
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Journal ArticleDOI
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes
TL;DR: An objective measure of genome quality is proposed that can be used to select genomes suitable for specific gene- and genome-centric analyses of microbial communities and is shown to provide accurate estimates of genome completeness and contamination and to outperform existing approaches.
DatasetDOI
CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes: supplemental material
TL;DR: Refining a marker set for lineage-specific Gene Loss and Duplication Estimates under Opal Stop Codon Recodings and Mean absolute error of completeness and contamination estimates determined using different universal- and domain-specific marker gene sets.
Journal ArticleDOI
The khmer software package: enabling efficient nucleotide sequence analysis.
Michael R. Crusoe,Hussien F. Alameldin,Sherine Awad,Elmar Boucher,Adam Caldwell,Reed A. Cartwright,Amanda Charbonneau,Bede Constantinides,Greg Edvenson,Scott Fay,Jacob Fenton,Thomas Fenzl,Jordan A. Fish,Leonor Garcia-Gutierrez,Phillip Garland,Jonathan Gluck,Ivan Gonzalez,Sarah Guermond,Jiarong Guo,Aditi Gupta,Joshua R. Herr,Adina Howe,Alex Hyer,Andreas Härpfer,Luiz Irber,Rhys Kidd,David Lin,Justin Lippi,Tamer A. Mansour,Pamela McA'Nulty,Eric McDonald,Jessica E. Mizzi,Kevin D Murray,Joshua R. Nahum,Kaben G. Nanlohy,Alexander J. Nederbragt,Humberto Ortiz-Zuazaga,Jeramia Ory,Jason Pell,Charles Pepe-Ranney,Zachary N. Russ,Erich M. Schwarz,Camille Scott,Josiah Seaman,Scott Sievert,Jared T. Simpson,Connor T. Skennerton,James S. Spencer,Ramakrishnan Srinivasan,Daniel S. Standage,James A. Stapleton,Susan R. Steinman,Joe Stein,Benjamin R Taylor,Will Trimble,Heather L. Wiencko,Michael Wright,Brian Wyss,Qingpeng Zhang,en zyme,C. Titus Brown +60 more
TL;DR: Khmer as discussed by the authors is a free software library for working efficiently with fixed length DNA words, or k-mers, which provides implementations of a probabilistic k-mer counting data structure, a compressible De Bruijn graph representation, De Bruhen graph partitioning, and digital normalization.
Journal ArticleDOI
An expanded genomic representation of the phylum cyanobacteria.
Rochelle M. Soo,Connor T. Skennerton,Yuji Sekiguchi,Michael Imelfort,Samuel J. Paech,Paul G. Dennis,Jason A. Steen,Donovan H. Parks,Gene W. Tyson,Philip Hugenholtz +9 more
TL;DR: It is proposed that the Melainabacteria is a class within the phylogenetically defined Cyanobacteria based on robust monophyly and shared ancestral traits with photosynthetic representatives, consistent with theories that photosynthesis occurred late in the Cyanob bacteria and involved extensive lateral gene transfer.
Journal ArticleDOI
Crass: identification and reconstruction of CRISPR from unassembled metagenomic data
TL;DR: Using Crass, the increased sensitivity, specificity and speed of Crass will facilitate comprehensive analysis of CRISPRs in metagenomic data sets, increasing the understanding of phage-host interactions and co-evolution within microbial communities.