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: InSilicoSeq

https://packages.ecosyste.ms/registries/pypi.org/packages/InSilicoSeq

a sequencing simulator
37 versions
Latest release: over 1 year ago
271 downloads last month

Papers Mentioning InSilicoSeq 17

10.1186/s12859-019-2684-x

From trash to treasure: detecting unexpected contamination in unmapped NGS data
Cited by: 42
Author(s): Mara Sangiovanni, Ilaria Granata, Amarinder Singh Thind, Mario Rosario Guarracino
Software Mentions: 7
Published: over 5 years ago

10.1128/mSystems.00811-21

Separation of Donor and Recipient Microbial Diversity Allows Determination of Taxonomic and Functional Features of Gut Microbiota Restructuring following Fecal Transplantation
Cited by: 4
Author(s): Evgenii I. Olekhnovich, A. B. Ivanov, Vladimir Ulyantsev, Elena Ilina
Software Mentions: 7
Published: over 3 years ago

10.1093/gigascience/giaa111

IDseq—An open source cloud-based pipeline and analysis service for metagenomic pathogen detection and monitoring
Cited by: 134
Author(s): Katrina Kalantar, Tiago Rodrigues De Carvalho, Charles F. A. de Bourcy, Boris Dimitrov, Greg Dingle, Rebecca Egger, Julie Han, Olivia B. Holmes, Yun Fang Juan, Ryan J. King, Andrey Kislyuk, Michael Lin, Maria Mariano, Todd Morse, Lucia V. Reynoso, David Rissato Cruz, Jonathan Sheu, Jennifer Tang, James Wang, Mark A. Zhang, Emily Zhong, Vida Ahyong, Sreyngim Lay, Sophana Chea, Jennifer A. Bohl, Jessica E. Manning, Cristina M. Tato, Joseph L. DeRisi
Software Mentions: 4
Published: about 4 years ago

10.1186/s12859-021-04153-0

DR2S: an integrated algorithm providing reference-grade haplotype sequences from heterozygous samples
Cited by: 3
Author(s): Steffen Klasberg, Alexander H. Schmidt, Vinzenz Lange, Gerhard Schöfl
Software Mentions: 4
Published: over 3 years ago

10.1186/s40168-019-0735-1

Identification of discriminatory antibiotic resistance genes among environmental resistomes using extremely randomized tree algorithm
Cited by: 34
Author(s): Suraj Gupta, Gustavo Arango-Argoty, Liqing Zhang, Amy Pruden, Peter J. Vikesland
Software Mentions: 3
Published: over 5 years ago

10.1186/s12859-020-03665-5

SimuSCoP: reliably simulate Illumina sequencing data based on position and context dependent profiles
Cited by: 11
Author(s): Zhenhua Yu, Fang Du, Rongjun Ban, Yuanwei Zhang
Software Mentions: 3
Published: over 4 years ago

10.1371/journal.pgen.1009242

Accurate mapping of mitochondrial DNA deletions and duplications using deep sequencing
Cited by: 36
Author(s): Swaraj Basu, Xie Xie, Jay P. Uhler, Carola Hedberg‐Oldfors, Dusanka Milenkovic, Olivier Baris, Sammy Kimoloi, Stanka Matic, James B. Stewart, Nils-Göran Larsson, Rudolf J. Wiesner, Anders Oldfors, Claes M. Gustafsson, Maria Falkenberg, Erik Larsson
Software Mentions: 3
Published: almost 4 years ago

10.3389/fgene.2021.648229

A Benchmark of Genetic Variant Calling Pipelines Using Metagenomic Short-Read Sequencing
Cited by: 13
Author(s): Sergio Andreu‐Sánchez, Lianmin Chen, Daoming Wang, Hannah E. Augustijn, Alexandra Zhernakova, Jingyuan Fu
Software Mentions: 3
Published: over 3 years ago

10.1093/bioinformatics/bty630

Simulating Illumina metagenomic data with InSilicoSeq
Cited by: 116
Author(s): Hadrien Gourlé, Oskar Karlsson Lindsjö, Juliette Hayer, Erik Bongcam‐Rudloff
Software Mentions: 2
Published: over 6 years ago

10.3390/pathogens9030204

Improved Metagenomic Taxonomic Profiling Using a Curated Core Gene-Based Bacterial Database Reveals Unrecognized Species in the Genus Streptococcus
Cited by: 9
Author(s): Mauricio Chalita, Seung Min Ha, Yeong Ouk Kim, Hyun-Seok Oh, Seok-Hwan Yoon, Jongsik Chun
Software Mentions: 2
Published: over 4 years ago

10.1371/journal.pcbi.1007781

PlasClass improves plasmid sequence classification
Cited by: 57
Author(s): David Pellow, Itzik Mizrahi, Ron Shamir
Software Mentions: 2
Published: over 4 years ago

10.1186/s12859-021-04242-0

Simulation study and comparative evaluation of viral contiguous sequence identification tools
Cited by: 15
Author(s): Cody Glickman, Jo Hendrix, Michael Strong
Software Mentions: 2
Published: over 3 years ago

10.1186/s12859-020-3372-6

Simulating metagenomic stable isotope probing datasets with MetaSIPSim
Cited by: 15
Author(s): Samuel E. Barnett, Daniel H. Buckley
Software Mentions: 2
Published: almost 5 years ago

10.3389/fmicb.2020.585622

Metagenomic Association Analysis of Gut Symbiont Limosilactobacillus reuteri Without Host-Specific Genome Isolation
Cited by: 4
Author(s): Sein Park, Martin Steinegger, Ho-Seong Cho, Jongsik Chun
Software Mentions: 2
Published: about 4 years ago

10.1186/s13073-020-00798-3

PathoSPOT genomic epidemiology reveals under-the-radar nosocomial outbreaks
Cited by: 11
Author(s): Ana Berbel Caban, Theodore R. Pak, Ajay Obla, Amy C. Dupper, Kieran I. Chacko, Lindsey Fox, Alexandra Mills, Brianne Ciferri, Irina Oussenko, Colleen Beckford, Marilyn Chung, Robert Sebra, Melissa Smith, Sarah Conolly, Gopi Patel, Andrew Kasarskis, Mitchell J. Sullivan, Deena R. Altman, Harm van Bakel
Software Mentions: 2
Published: about 4 years ago

10.1186/s40168-021-01015-y

Accurate and sensitive detection of microbial eukaryotes from whole metagenome shotgun sequencing
Cited by: 49
Author(s): Abigail Lind, Katherine S. Pollard
Software Mentions: 1
Published: almost 4 years ago

10.1186/s13015-021-00185-6

Improving metagenomic binning results with overlapped bins using assembly graphs
Cited by: 10
Author(s): Vijini Mallawaarachchi, Anuradha Wickramarachchi, Yu Lin
Software Mentions: 1
Published: over 3 years ago