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: fastaq

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

fastAQ is a very and super lightweight package for working with FASTA/FASTQ sequences
2 versions
Latest release: about 10 years ago
22 downloads last month

Papers Mentioning fastaq 15

A workflow with R: Phylogenetic analyses and visualizations using mitochondrial cytochrome b gene sequences
Cited by: 13
Author(s): Emine Toparslan, Kemal Karabağ, Uğur Bilge
Software Mentions: 24
Published: almost 4 years ago

10.1099/mgen.0.000131

ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads
Cited by: 370
Author(s): Martin Hunt, Alison E. Mather, Leonor Sánchez-Busó, Andrew J. Page, Julian Parkhill, Jacqueline A. Keane, Simon R. Harris
Software Mentions: 12
Published: about 7 years ago

10.1099/mgen.0.000569

Genomic and temporal analyses of Mycobacterium bovis in southern Brazil
Cited by: 7
Author(s): Rudielle de Arruda Rodrigues, Flábio R. Araújo, Alberto M. R. Dávila, Rodrigo Nestor Etges, Julian Parkhill, Andries J. van Tonder
Software Mentions: 4
Published: over 3 years ago

10.1093/ve/vey007

Easy and accurate reconstruction of whole HIV genomes from short-read sequence data with shiver
Cited by: 51
Author(s): Chris Wymant, François Blanquart, Tanya Golubchik, Astrid Gall, Margreet Bakker, Daniela Bezemer, Nicholas J. Croucher, Matthew Hall, Mariska Hillebregt, Swee Hoe Ong, Oliver Ratmann, Jan Albert, Norbert Bannert, Jacques Fellay, Katrien Fransen, Annabelle Gourlay, M Kate Grabowski, Barbara Gunsenheimer‐Bartmeyer, Huldrych F Günthard, Pia Kivelä, Roger D. Kouyos, Oliver Laeyendecker, Kirsi Liitsola, Laurence Meyer, Kholoud Porter, Matti Ristola, Ard van Sighem, Ben Berkhout, Marion Cornelissen, Paul Kellam, Peter Reiss, Christophe Fraser
Software Mentions: 4
Published: almost 7 years ago

10.1099/mgen.0.000085

Comparison of bacterial genome assembly software for MinION data and their applicability to medical microbiology
Cited by: 27
Author(s): Kim Judge, Martin Hunt, Sandra Reuter, Alan S. Tracey, Michael A. Quail, Julian Parkhill, Sharon J. Peacock
Software Mentions: 3
Published: about 8 years ago

10.1099/mgen.0.000124

Comparison of classical multi-locus sequence typing software for next-generation sequencing data
Cited by: 27
Author(s): Andrew J. Page, Nabil-Fareed Alikhan, Heather Carleton, Torsten Seemann, Jacqueline A. Keane, Lee S. Katz
Software Mentions: 3
Published: over 7 years ago

10.1186/s13059-021-02465-1

NucHMM: a method for quantitative modeling of nucleosome organization identifying functional nucleosome states distinctly associated with splicing potentiality
Cited by: 5
Author(s): Kun Fang, Tianbao Li, Yufei Huang, Victor X. Jin
Software Mentions: 3
Published: about 3 years ago

10.1093/gigascience/gix123

BS-virus-finder: virus integration calling using bisulfite sequencing data
Cited by: 5
Author(s): Shengjie Gao, Xuesong Hu, Fengping Xu, Changduo Gao, Kai Xiong, Xiao Zhao, Haixiao Chen, Shancen Zhao, Mengyao Wang, Deliang Fu, Xiaohui Zhao, Jie Bai, Likai Mao, Bo Li, Song Wu, Jian Wang, Shengbin Li, Huangming Yang, Lars Bolund, Christian N. S. Pedersen
Software Mentions: 2
Published: almost 7 years ago

10.1128/mBio.00603-19

Barcoded Consortium Infections Resolve Cell Type-Dependent Salmonella enterica Serovar Typhimurium Entry Mechanisms
Cited by: 11
Author(s): Maria Letizia Di Martino, Viktor Ek, Wolf‐Dietrich Hardt, Jens Eriksson, Mikael E. Sellin
Software Mentions: 1
Published: over 5 years ago

10.3390/microorganisms9020269

Intracellular Bacteria in Plants: Elucidation of Abundant and Diverse Cytoplasmic Bacteria in Healthy Plant Cells Using In Vitro Cell and Callus Cultures
Cited by: 11
Author(s): Pious Thomas, Christopher M. M. Franco
Software Mentions: 1
Published: almost 4 years ago

10.3390/v12020150

Genomic Characterization, Formulation and Efficacy in Planta of a Siphoviridae and Podoviridae Protection Cocktail against the Bacterial Plant Pathogens Pectobacterium spp.
Cited by: 14
Author(s): Maja Zaczek-Moczydlowska, Gillian Young, James Trudgett, Colin C. Fleming, Katrina Campbell, Richard O’Hanlon
Software Mentions: 1
Published: almost 5 years ago

10.1371/journal.pone.0146275

Individualized Mutation Detection in Circulating Tumor DNA for Monitoring Colorectal Tumor Burden Using a Cancer-Associated Gene Sequencing Panel
Cited by: 40
Author(s): Kei Sato, Tsuyoshi Hachiya, Takeshi Iwaya, Kohei Kume, Teppei Matsuo, Koichiro Kawasaki, Yukito Abiko, Risaburo Akasaka, Takayuki Matsumoto, Koki Otsuka, Satoshi Nishizuka
Software Mentions: 1
Published: almost 9 years ago

10.1371/journal.pone.0059543

Boron Stress Responsive MicroRNAs and Their Targets in Barley
Cited by: 79
Author(s): Esma Ozhuner, Vahap Eldem, Ahmet İpek, Sezer Okay, Serdal Sakçalı, Baohong Zhang, Hatice Boke, Turgay Ünver
Software Mentions: 1
Published: over 11 years ago

10.1038/s41598-020-77386-3

Identification of a novel enzyme from E. pacifica that acts as an eicosapentaenoic 8R-LOX and docosahexaenoic 10R-LOX
Cited by: 2
Author(s): Sayaka Yuki, Aiko Uemura, Mayuka Hakozaki, Akira Yano, Masato Abe, Yoshihisa Misawa, Naomichi Baba, Hidetoshi Yamada
Software Mentions: 1
Published: almost 4 years ago

10.1186/s13075-016-1037-7

Collagen epitope expression on B cells is sufficient to confer tolerance to collagen-induced arthritis
Cited by: 7
Author(s): S. Andersson, Tove Eneljung, Sara Tengvall, Pernilla Jirholt, Anna Stern, Louise Henningsson, Bibo Liang, Katrin Thorarinsdottir, Jan Kihlberg, Rikard Holmdahl, Inga‐Lill Mårtensson, Kenth Gustafsson, Inger Gjertsson
Software Mentions: 1
Published: over 8 years ago