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: vg
https://packages.ecosyste.ms/registries/pypi.org/packages/vg
Linear algebra for humans: a very good vector-geometry and linear-algebra toolbelt
25 versions
Latest release: over 3 years ago
11 dependent packages
8,070 downloads last month
Papers Mentioning vg 34
10.1186/s13059-021-02473-1
Pandora: nucleotide-resolution bacterial pan-genomics with reference graphsCited 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
10.1186/s13059-020-1941-7
Genotyping structural variants in pangenome graphs using the vg toolkitCited by: 136
Author(s): Glenn Hickey, David Heller, Jean Monlong, Jonas Andreas Sibbesen, Jouni Sirén, Jordan M. Eizenga, Eric T. Dawson, Erik Garrison, Adam M. Novak, Benedict Paten
Software Mentions: 9
Published: almost 5 years ago
10.1186/s13059-020-02038-8
Personalized and graph genomes reveal missing signal in epigenomic dataCited by: 25
Author(s): Cristian Groza, Tony Kwan, Nicole Soranzo, Tomi Pastinen, Guillaume Bourque
Software Mentions: 8
Published: over 4 years ago
10.1186/s12859-019-3145-2
MoMI-G: modular multi-scale integrated genome graph browserCited by: 20
Author(s): Toshiyuki Yokoyama, Yoshitaka Sakamoto, Masahide Seki, Yutaka Suzuki, Masahiro Kasahara
Software Mentions: 8
Published: about 5 years ago
10.1186/s12859-019-3122-9
Third international conference “Bioinformatics: from Algorithms to Applications” (BiATA 2019)Cited by: 1
Author(s):
Software Mentions: 6
Published: about 5 years ago
10.1186/s13059-020-02160-7
Removing reference bias and improving indel calling in ancient DNA data analysis by mapping to a sequence variation graphCited by: 33
Author(s): Rui Martiniano, Erik Garrison, Eppie R. Jones, Andrea Manica, Richard Durbin
Software Mentions: 6
Published: about 4 years ago
10.1186/s13059-020-02157-2
GraphAligner: rapid and versatile sequence-to-graph alignmentCited by: 76
Author(s): Mikko Rautiainen, Tobias Marschall
Software Mentions: 5
Published: about 4 years ago
10.1371/journal.pcbi.1006731
Graph Peak Caller: Calling ChIP-seq peaks on graph-based reference genomesCited by: 19
Author(s): Ivar Grytten, Knut Dagestad Rand, Alexander J. Nederbragt, Geir Storvik, Ingrid K. Glad, Geir Kjetil Sandve
Software Mentions: 5
Published: almost 6 years ago
10.1186/s13059-021-02474-0
Gramtools enables multiscale variation analysis with genome graphsCited by: 13
Author(s): Brice Letcher, Martin Hunt, Zamin Iqbal
Software Mentions: 5
Published: about 3 years ago
10.12688/f1000research.15895.2
NovoGraph: Human genome graph construction from multiple long-read de novo assembliesCited by: 5
Author(s): Evan Biederstedt, Jeffrey C. Oliver, Nancy F. Hansen, Aarti Jajoo, Nathan Dunn, Andrew Olson, Ben Busby, Alexander Dilthey
Software Mentions: 4
Published: almost 6 years ago
10.1186/s12859-019-3115-8
GenGraph: a python module for the simple generation and manipulation of genome graphsCited by: 4
Author(s): Jon Ambler, Shandukani Mulaudzi, Nicola Mulder
Software Mentions: 4
Published: about 5 years ago
10.7554/eLife.67615
Local adaptation and archaic introgression shape global diversity at human structural variant lociCited by: 27
Author(s): Shouqing Yan, Rachel M. Sherman, Dylan J. Taylor, Divya R. Nair, Andrew N Bortvin, Michael C. Schatz, Rajiv C. McCoy
Software Mentions: 4
Published: about 3 years ago
10.3390/biom10040509
The Influence of Varying Fluorination Patterns on the Thermodynamics and Kinetics of Benzenesulfonamide Binding to Human Carbonic Anhydrase IICited by: 7
Author(s): Steffen Glöckner, K. Ngo, Björn Wagner, A. Heine, G. Klebe
Software Mentions: 3
Published: over 4 years ago
10.1186/s12859-020-03590-7
SPAligner: alignment of long diverged molecular sequences to assembly graphsCited by: 12
Author(s): Tatiana Dvorkina, Dmitry Antipov, Anton Korobeynikov, Sergey Nurk
Software Mentions: 3
Published: over 4 years ago
10.12688/f1000research.19630.2
A strategy for building and using a human reference pangenomeCited by: 5
Author(s): Bastien Llamas, Giuseppe Narzisi, Valérie Schneider, Peter A. Audano, Evan Biederstedt, Lon Blauvelt, Peter J. Bradbury, Xian Chang, Chen-Shan Chin, Arkarachai Fungtammasan, Wayne E. Clarke, Alan Cleary, Jana Ebler, Jordan Eizenga, Jonas Andreas Sibbesen, Charles Markello, Erik Garrison, Shilpa Garg, Glenn Hickey, Gerard R. Lazo, Michael Lin, Medhat Mahmoud, Tobias Marschall, Ilia Minkin, Jean Monlong, Rajeeva Musunuri, Sagayamary Sagayaradj, Adam M. Novak, Mikko Rautiainen, Allison Regier, Fritz J. Sedlazeck, Jouni Sirén, Yassine Souilmi, Justin Wagner, Travis Wrightsman, Toshiyuki Yokoyama, Qiandong Zeng, Justin M. Zook, Benedict Paten, Ben Busby
Software Mentions: 3
Published: over 3 years ago
10.1016/j.isci.2021.102755
Linearization of genome sequence graphs revisitedCited by: 0
Author(s): A. Lisiecka, Norbert Dojer
Software Mentions: 2
Published: over 3 years ago
10.1186/s13059-020-02229-3
Reference flow: reducing reference bias using multiple population genomesCited by: 29
Author(s): Nae-Chyun Chen, Brad Solomon, Taher Mun, Sheila Iyer, Ben Langmead
Software Mentions: 2
Published: almost 4 years ago
10.1186/s13059-020-02105-0
Bovine breed-specific augmented reference graphs facilitate accurate sequence read mapping and unbiased variant discoveryCited by: 30
Author(s): Danang Crysnanto, Hubert Pausch
Software Mentions: 2
Published: over 4 years ago
10.1093/bioinformatics/btab281
Constructing small genome graphs via string compressionCited by: 2
Author(s): Yutong Qiu, Carl Kingsford
Software Mentions: 2
Published: over 3 years ago
10.1093/dnares/dsaa030
Building pan-genome infrastructures for crop plants and their use in association geneticsCited by: 49
Author(s): Murukarthick Jayakodi, Mona Schreiber, Nils Stein, Martin Mascher
Software Mentions: 1
Published: almost 4 years ago
10.1186/s12864-017-4401-3
seq-seq-pan: building a computational pan-genome data structure on whole genome alignmentCited by: 25
Author(s): Christine Jandrasits, Piotr Wojtek Dabrowski, Stephan Fuchs, Bernhard Y. Renard
Software Mentions: 1
Published: almost 7 years ago
10.1186/s12864-020-6685-y
Assessing graph-based read mappers against a baseline approach highlights strengths and weaknesses of current methodsCited by: 11
Author(s): Ivar Grytten, Knut Dagestad Rand, Alexander Johan Nederbragt, Geir Kjetil Sandve
Software Mentions: 1
Published: over 4 years ago
10.1186/s12911-019-0960-3
Fast read alignment with incorporation of known genomic variantsCited by: 0
Author(s): Hongzhe Guo, Bo Liu, Dengfeng Guan, Yilei Fu, Yadong Wang
Software Mentions: 1
Published: almost 5 years ago
10.1093/bioinformatics/btab077
Detecting high-scoring local alignments in pangenome graphsCited by: 6
Author(s): Tizian Schulz, Roland Wittler, Sven Rahmann, Faraz Hach, Jens Stoye
Software Mentions: 1
Published: almost 4 years ago
10.1093/bioinformatics/btz162
Bit-parallel sequence-to-graph alignmentCited by: 47
Author(s): Mikko Rautiainen, Veli Mäkinen, Tobias Marschall
Software Mentions: 1
Published: over 5 years ago
10.1093/bioinformatics/btz597
Sequence tube maps: making graph genomes intuitive to commutersCited by: 27
Author(s): Wolfgang Beyer, Adam M. Novak, Glenn Hickey, Jeffrey Chan, Vanessa Tan, Benedict Paten, Daniel R. Zerbino
Software Mentions: 1
Published: over 5 years ago
10.1093/bioinformatics/btaa265
Vargas: heuristic-free alignment for assessing linear and graph read alignersCited by: 13
Author(s): Charlotte A. Darby, Ravi Gaddipati, Michael C. Schatz, Ben Langmead
Software Mentions: 1
Published: over 4 years ago
10.7717/peerj.11884
<tt>StrainFLAIR</tt>: strain-level profiling of metagenomic samples using variation graphsCited by: 3
Author(s): Kévin Da Silva, Nicolas Pons, Magali Berland, Florian Plaza Oñate, Mathieu Almeida, Pierre Peterlongo
Software Mentions: 1
Published: about 3 years ago
10.1371/journal.pcbi.1007527
Computational pan-genome mapping and pairwise SNP-distance improve detection of Mycobacterium tuberculosis transmission clustersCited by: 13
Author(s): Christine Jandrasits, Stefan Kröger, Walter Haas, Bernhard Y. Renard
Software Mentions: 1
Published: almost 5 years ago
10.1186/s13015-017-0109-9
A graph extension of the positional Burrows–Wheeler transform and its applicationsCited by: 31
Author(s): Adam M. Novak, Erik Garrison, Benedict Paten
Software Mentions: 1
Published: over 7 years ago
10.1186/s13059-020-01963-y
CHOP: haplotype-aware path indexing in population graphsCited by: 7
Author(s): Tom Mokveld, Jasper Linthorst, Zaid Al-Ars, Henne Holstege, Marcel J. T. Reinders
Software Mentions: 1
Published: over 4 years ago
10.1186/s13059-020-02168-z
The design and construction of reference pangenome graphs with minigraphCited by: 170
Author(s): Heng Li, Xiaowen Feng, Chong Chu
Software Mentions: 1
Published: about 4 years ago
10.1186/s13059-021-02383-2
Impacts of allopolyploidization and structural variation on intraspecific diversification in Brassica rapaCited by: 66
Author(s): Xiaohua Cai, Chang Lei, Tingting Zhang, Haixu Chen, Lei Zhang, Runmao Lin, Jiansheng Liang, Jian Wu, Michael Freeling, Xiaowu Wang
Software Mentions: 1
Published: over 3 years ago
10.1016/j.isci.2019.07.011
MALVA: Genotyping by Mapping-free ALlele Detection of Known VAriantsCited by: 25
Author(s): Luca Denti, Marco Previtali, Giulia Bernardini, Alexander Schönhuth, Paola Bonizzoni
Software Mentions: 1
Published: over 5 years ago