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: medaka

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

Neural network sequence error correction.
83 versions
Latest release: about 1 year ago
1,736 downloads last month

Papers Mentioning medaka 15

Pandora: nucleotide-resolution bacterial pan-genomics with reference graphs
Cited by: 20
Author(s): Rachel Colquhoun, Michael B. Hall, Leandro Lima, Leah W. Roberts, Kerri M. Malone, Martin Hunt, Brice Letcher, Jane Hawkey, Sophie George, Louise Pankhurst, Zamin Iqbal
Software Mentions: 10
Published: about 3 years ago

10.1093/femsec/fiab127

Microbial characterisation and Cold-Adapted Predicted Protein (CAPP) database construction from the active layer of Greenland's permafrost
Cited by: 1
Author(s): Gilda Varliero, Muhammad Rafiq, Swati Singh, Annabel Summerfield, Fotis Sgouridis, Donald A. Cowan, Gary Barker
Software Mentions: 10
Published: about 3 years ago

10.1371/journal.pcbi.1008716

Metagenomics workflow for hybrid assembly, differential coverage binning, metatranscriptomics and pathway analysis (MUFFIN)
Cited by: 14
Author(s): Renaud Van Damme, Martin Hölzer, Adrian Viehweger, Bettina Müller, Erik Bongcam‐Rudloff, Christian Brandt
Software Mentions: 8
Published: almost 4 years ago

10.1128/MRA.00333-21

Genome Sequences of Equine Herpesvirus 1 Strains from a European Outbreak of Neurological Disorders Linked to a Horse Gathering in Valencia, Spain, in 2021
Cited by: 10
Author(s): Nick Vereecke, Flora Carnet, Stéphane Pronost, Katleen Vanschandevijl, Sebastiaan Theuns, Hans Nauwynck
Software Mentions: 3
Published: over 3 years ago

10.1128/JCM.00920-20

Rapid and Sensitive Direct Detection and Identification of Poliovirus from Stool and Environmental Surveillance Samples by Use of Nanopore Sequencing
Cited by: 28
Author(s): Alexander Shaw, Manasi Majumdar, Catherine Troman, Áine O’Toole, Blossom Benny, Dilip Abraham, Ira Praharaj, Gagandeep Kang, Salman Sharif, Muhammad Masroor Alam, Shahzad Shaukat, Mehar Angez, Adnan Khurshid, Nayab Mahmood, Yasir Arshad, Lubna Rehman, Ghulam Mujtaba, Ribqa Akthar, Muhammad Salman, Dimitra Klapsa, Yara Hajarha, Humayun Asghar, Ananda S Bandyopadhyay, Andrew Rambaut, Javier Martı́n, Nicholas C Grassly
Software Mentions: 3
Published: about 4 years ago

10.1128/MRA.00055-20

Complete Genome Sequence of Pseudomonas putida Strain TS312, Harboring an HdtS-Type N -Acyl-Homoserine Lactone Synthase, Isolated from a Paper Mill
Cited by: 2
Author(s): Ayaka Hosoe, Toshikazu Suenaga, Takumi Sugi, Taro Iizumi, Naohiro Nagai, Akihiko Terada
Software Mentions: 2
Published: over 4 years ago

10.1186/s13073-021-00839-5

CoronaHiT: high-throughput sequencing of SARS-CoV-2 genomes
Cited by: 89
Author(s): Dave Baker, Alp Aydin, Thanh Le-Viet, Gemma L. Kay, Steven Rudder, Leonardo de Oliveira Martins, Ana P. Tedim, Anastasia Kolyva, María Díaz, Nabil Fareed Alikhan, Lizzie Meadows, Andrew Bell, Ana Victoria Gutiérrez, Alexander J. Trotter, Nicholas Thomson, Rachel Gilroy, Luke Griffith, Evelien M. Adriaenssens, Rachael Stanley, Ian G. Charles, Ngozi Elumogo, John Wain, Reenesh Prakash, Emma Meader, Alison E. Mather, Mark A. Webber, Samir Dervisevic, Andrew J. Page, Justin O’Grady
Software Mentions: 1
Published: almost 4 years ago

10.1080/19490976.2020.1826761

Linear and branched β-Glucans degrading enzymes from versatile Bacteroides uniformis JCM 13288T and their roles in cooperation with gut bacteria
Cited by: 17
Author(s): Ravindra Singh, Sivasubramanian Rajarammohan, Raksha Thakur, Mohsin Hassan
Software Mentions: 1
Published: about 4 years ago

10.1186/s12934-021-01586-3

Adaptive laboratory evolution accelerated glutarate production by Corynebacterium glutamicum
Cited by: 16
Author(s): Carina Prell, Tobias Busche, Christian Rückert, Lea Nolte, Christoph Brandenbusch, Volker F. Wendisch
Software Mentions: 1
Published: over 3 years ago

10.1016/j.isci.2020.101128

CONNET: Accurate Genome Consensus in Assembling Nanopore Sequencing Data via Deep Learning
Cited by: 5
Author(s): Yifan Zhang, Chi-Man Liu, Ho-fung Leung, Ruibang Luo, Tak-Wah Lam
Software Mentions: 1
Published: over 4 years ago

10.1128/MRA.00040-20

Complete Genome Sequence of the Cryptophycin-Producing Cyanobacterium Nostoc sp. Strain ATCC 53789
Cited by: 5
Author(s): Anna Tippelt, Tobias Busche, Christian Rückert, Markus Nett
Software Mentions: 1
Published: over 4 years ago

10.1128/MRA.00372-21

Chromosome-Level Genome Sequence of Aspergillus puulaauensis MK2, a Fungus Isolated from a Dead Hard Tick
Cited by: 1
Author(s): Taiki Futagami, K. Mori, Chihiro Kadooka, Hiroko Niihara, Kosuke Tashiro, Hiroyuki Tamaki, Tetsuya Tanaka
Software Mentions: 1
Published: about 3 years ago

10.1128/MRA.00507-19

Complete Genome Sequence of Bacillus mycoides TH26, Isolated from a Permafrost Thaw Gradient
Cited by: 5
Author(s): Tracie J. Haan, Scout McDougall, Devin M. Drown
Software Mentions: 1
Published: over 5 years ago

10.1128/MRA.00385-21

Chromosome-Level Genome Sequence of Aspergillus chevalieri M1, Isolated from Katsuobushi
Cited by: 1
Author(s): Chihiro Kadooka, K. Mori, Kayu Okutsu, Yumiko Yoshizaki, Kazunori Takamine, Kosuke Tashiro, Hiroyuki Tamaki, Taiki Futagami
Software Mentions: 1
Published: about 3 years ago

10.3389/fmicb.2021.651151

AmpliCoV: Rapid Whole-Genome Sequencing Using Multiplex PCR Amplification and Real-Time Oxford Nanopore MinION Sequencing Enables Rapid Variant Identification of SARS-CoV-2
Cited by: 24
Author(s): Annika Brinkmann, Sophie-Luisa Ulm, Steven Uddin, Sophie Förster, Dominique Seifert, Rainer Oehme, Merle Corty, Lars Schaade, Janine Michel, Andreas Nitsche
Software Mentions: 1
Published: over 3 years ago