Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Projects: pypi: illumina-utils

https://packages.ecosyste.ms/registries/pypi.org/packages/illumina-utils

A library and collection of scripts to work with Illumina paired-end data (for CASAVA 1.8+).
30 versions
Latest release: about 3 years ago
245 downloads last month

Papers Mentioning illumina-utils 22

10.1128/mBio.01054-19

Microbial Similarity between Students in a Common Dormitory Environment Reveals the Forensic Potential of Individual Microbial Signatures
Cited by: 28
Author(s): Miles Richardson, Neil Gottel, Jack A. Gilbert, Simon Lax
Software Mentions: 18
Published: about 5 years ago

10.7717/peerj.3472

Using high-throughput sequencing of ITS2 to describe Symbiodinium metacommunities in St. John, US Virgin Islands
Cited by: 50
Author(s): Ross Cunning, Ruth D. Gates, Peter J. Edmunds
Software Mentions: 14
Published: about 7 years ago

10.1128/mSystems.00068-21

Diverse Viruses in Deep-Sea Hydrothermal Vent Fluids Have Restricted Dispersal across Ocean Basins
Cited by: 14
Author(s): Elaina Thomas, R. Anderson, Viola Li, L Jenni Rogan, Julie A. Huber
Software Mentions: 11
Published: about 3 years ago

10.1186/s13059-020-02195-w

Functional and genetic markers of niche partitioning among enigmatic members of the human oral microbiome
Cited by: 107
Author(s): Alon Shaiber, Amy Willis, Tom O. Delmont, Simon Roux, Lin-Xing Chen, Abigail C. Schmid, Mahmoud Yousef, Andrea R. Watson, Karen Lolans, Özcan C. Esen, Sonny T. M. Lee, Nora Downey, Hilary G. Morrison, Floyd E. Dewhirst, Jessica L. Mark Welch, A. Murat Eren
Software Mentions: 8
Published: almost 4 years ago

10.7717/peerj.4320

Linking pangenomes and metagenomes: the Prochlorococcus metapangenome
Cited by: 272
Author(s): Tom O. Delmont, A. Murat Eren
Software Mentions: 6
Published: over 6 years ago

10.7554/eLife.36521

Experimental evaluation of the importance of colonization history in early-life gut microbiota assembly
Cited by: 129
Author(s): Inés Martínez, María X. Maldonado-Gómez, João Carlos Gomes-Neto, Hatem Kittana, Hua Ding, Robert Schmaltz, Payal Joglekar, Roberto Jiménez Cardona, Nathan L. Marsteller, Steven W. Kembel, Andrew K. Benson, Daniel A. Peterson, Amanda E. Ramer‐Tait, Jens Walter
Software Mentions: 5
Published: about 6 years ago

10.7717/peerj.1319

Anvi’o: an advanced analysis and visualization platform for ‘omics data
Cited by: 1,274
Author(s): A. Murat Eren, Özcan C. Esen, Christopher Quince, Joseph H. Vineis, Hilary G. Morrison, Mitchell L. Sogin, Tom O. Delmont
Software Mentions: 5
Published: almost 9 years ago

10.7717/peerj.7548

Genome-resolved insights into a novelSpiroplasmasymbiont of the Wheat Stem Sawfly (Cephus cinctus)
Cited by: 11
Author(s): Carl J. Yeoman, Laura M. Brutscher, Özcan C. Esen, Furkan Ibaoglu, Curtis Fowler, A. Murat Eren, Kevin W. Wanner, David K. Weaver
Software Mentions: 4
Published: about 5 years ago

10.7554/eLife.46497

Single-amino acid variants reveal evolutionary processes that shape the biogeography of a global SAR11 subclade
Cited by: 80
Author(s): Tom O. Delmont, Evan Kiefl, Ozsel Kilinc, Özcan C. Esen, Ismail Uysal, Michael S. Rappé, Steven Giovannoni, A. Murat Eren
Software Mentions: 3
Published: about 5 years ago

10.7717/peerj.1839

Identifying contamination with advanced visualization and analysis practices: metagenomic approaches for eukaryotic genome assemblies
Cited by: 86
Author(s): Tom O. Delmont, A. Murat Eren
Software Mentions: 3
Published: over 8 years ago

10.3389/fmicb.2019.01027

Designing and Engineering Methylorubrum extorquens AM1 for Itaconic Acid Production
Cited by: 20
Author(s): Chee Kent Lim, Juan C. Villada, Annie Chalifour, Maria F. Duran, Hsu Feng Lu, Patrick K. H. Lee
Software Mentions: 3
Published: over 5 years ago

10.3389/fmicb.2021.714920

Genomic Variation Influences Methanothermococcus Fitness in Marine Hydrothermal Systems
Cited by: 2
Author(s): Michael Hoffert, Rika E. Anderson, Julie Réveillaud, Leslie G. Murphy, Ramunas Stepanauskas, J. A. Huber
Software Mentions: 3
Published: about 3 years ago

10.3389/fmicb.2018.02485

Flexible Symbiotic Associations of Symbiodinium With Five Typical Coral Species in Tropical and Subtropical Reef Regions of the Northern South China Sea
Cited by: 28
Author(s): Sanqiang Gong, Guangjun Chai, Yilin Xiao, Lijia Xu, Kefu Yu, Jinlong Li, Fang Liu, Hao Cheng, Fengli Zhang, Baolin Liao, Zhiyong Li
Software Mentions: 3
Published: almost 6 years ago

10.1128/mBio.01228-21

Alternative Transmission Patterns in Independently Acquired Nutritional Cosymbionts of Dictyopharidae Planthoppers
Cited by: 15
Author(s): Anna Michalik, Diego Castillo Franco, Michał Kobiałka, Teresa Szklarzewicz, Adam Stroiński, Piotr Łukasik
Software Mentions: 3
Published: about 3 years ago

10.1128/mSystems.00889-21

A Combination of Metagenomic and Cultivation Approaches Reveals Hypermutator Phenotypes within Vibrio cholerae-Infected Patients
Cited by: 7
Author(s): Inès Levade, Ashraful Islam Khan, Fahima Chowdhury, Stephen B. Calderwood, Edward T. Ryan, Jason B. Harris, Regina C. LaRocque, Taufiqur Rahman Bhuiyan, Firdausi Qadri, Ana A. Weil, Ben Shapiro
Software Mentions: 3
Published: about 3 years ago

10.3389/fmicb.2015.01090

Genome reconstructions indicate the partitioning of ecological functions inside a phytoplankton bloom in the Amundsen Sea, Antarctica
Cited by: 39
Author(s): Tom O. Delmont, A. Murat Eren, Joseph H. Vineis, Anton F. Post
Software Mentions: 2
Published: almost 9 years ago

10.1128/mSystems.00159-19

Elucidating Syntrophic Butyrate-Degrading Populations in Anaerobic Digesters Using Stable-Isotope-Informed Genome-Resolved Metagenomics
Cited by: 18
Author(s): Ryan M. Ziels, Masaru K. Nobu, Diana Z. Sousa
Software Mentions: 2
Published: about 5 years ago

10.1128/mSystems.00673-19

Selection Is a Significant Driver of Gene Gain and Loss in the Pangenome of the Bacterial Genus Sulfurovum in Geographically Distinct Deep-Sea Hydrothermal Vents
Cited by: 33
Author(s): Alief Moulana, R. Anderson, Caroline S. Fortunato, Julie A. Huber
Software Mentions: 2
Published: over 4 years ago

10.1128/mSystems.00342-19

Genomic Evidence for Simultaneous Optimization of Transcription and Translation through Codon Variants in the pmoCAB Operon of Type Ia Methanotrophs
Cited by: 7
Author(s): Juan C. Villada, Maria F. Duran, Patrick K. H. Lee
Software Mentions: 2
Published: about 5 years ago

10.1186/s40168-021-01045-6

Niche partitioning in the Rimicaris exoculata holobiont: the case of the first symbiotic Zetaproteobacteria
Cited by: 19
Author(s): Marie-Anne Cambon-Bonavita, Johanne Aubé, Valérie Cueff-Gauchard, Julie Réveillaud
Software Mentions: 2
Published: over 3 years ago

10.3389/fmicb.2020.569354

Disease Diagnostics and Potential Coinfections by Vibrio coralliilyticus During an Ongoing Coral Disease Outbreak in Florida
Cited by: 45
Author(s): Blake Ushijima, Julie Meyer, Sharon Thompson, Kelly A. Pitts, Michael F. Marusich, Jessica Tittl, Elizabeth Weatherup, Jacqueline Reu, Raquel Wetzell, Greta S. Aeby, Claudia C. Häse, Valerie J. Paul
Software Mentions: 1
Published: almost 4 years ago

10.7717/peerj.4735

Salt marsh sediment bacterial communities maintain original population structure after transplantation across a latitudinal gradient
Cited by: 12
Author(s): Angus Angermeyer, Sarah C. Crosby, J. A. Huber
Software Mentions: 1
Published: over 6 years ago