pypi: vg | Projects | Ecosyste.ms: Papers

10.1186/s13059-021-02473-1

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: over 3 years ago

10.1186/s13059-020-1941-7

Genotyping structural variants in pangenome graphs using the vg toolkit
Cited 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 data
Cited 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 browser
Cited 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 graph
Cited by: 33
Author(s): Rui Martiniano, Erik Garrison, Eppie R. Jones, Andrea Manica, Richard Durbin
Software Mentions: 6
Published: over 4 years ago

10.1186/s13059-020-02157-2

GraphAligner: rapid and versatile sequence-to-graph alignment
Cited by: 76
Author(s): Mikko Rautiainen, Tobias Marschall
Software Mentions: 5
Published: over 4 years ago

10.1371/journal.pcbi.1006731

Graph Peak Caller: Calling ChIP-seq peaks on graph-based reference genomes
Cited 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 graphs
Cited by: 13
Author(s): Brice Letcher, Martin Hunt, Zamin Iqbal
Software Mentions: 5
Published: over 3 years ago

10.12688/f1000research.15895.2

NovoGraph: Human genome graph construction from multiple long-read de novo assemblies
Cited 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: about 6 years ago

10.1186/s12859-019-3115-8

GenGraph: a python module for the simple generation and manipulation of genome graphs
Cited 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 loci
Cited 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: over 3 years ago

10.3390/biom10040509

The Influence of Varying Fluorination Patterns on the Thermodynamics and Kinetics of Benzenesulfonamide Binding to Human Carbonic Anhydrase II
Cited by: 7
Author(s): Steffen Glöckner, K. Ngo, Björn Wagner, A. Heine, G. Klebe
Software Mentions: 3
Published: almost 5 years ago

10.1186/s12859-020-03590-7

SPAligner: alignment of long diverged molecular sequences to assembly graphs
Cited 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 pangenome
Cited 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 revisited
Cited 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 genomes
Cited 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 discovery
Cited 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 compression
Cited 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 genetics
Cited 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 alignment
Cited 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 methods
Cited 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 variants
Cited by: 0
Author(s): Hongzhe Guo, Bo Liu, Dengfeng Guan, Yilei Fu, Yadong Wang
Software Mentions: 1
Published: about 5 years ago

10.1093/bioinformatics/btab077

Detecting high-scoring local alignments in pangenome graphs
Cited 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 alignment
Cited by: 47
Author(s): Mikko Rautiainen, Veli Mäkinen, Tobias Marschall
Software Mentions: 1
Published: almost 6 years ago

10.1093/bioinformatics/btz597

Sequence tube maps: making graph genomes intuitive to commuters
Cited 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 aligners
Cited 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 graphs
Cited by: 3
Author(s): Kévin Da Silva, Nicolas Pons, Magali Berland, Florian Plaza Oñate, Mathieu Almeida, Pierre Peterlongo
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pcbi.1007527

Computational pan-genome mapping and pairwise SNP-distance improve detection of Mycobacterium tuberculosis transmission clusters
Cited by: 13
Author(s): Christine Jandrasits, Stefan Kröger, Walter Haas, Bernhard Y. Renard
Software Mentions: 1
Published: about 5 years ago

10.1186/s13015-017-0109-9

A graph extension of the positional Burrows–Wheeler transform and its applications
Cited 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 graphs
Cited by: 7
Author(s): Tom Mokveld, Jasper Linthorst, Zaid Al-Ars, Henne Holstege, Marcel J. T. Reinders
Software Mentions: 1
Published: almost 5 years ago

10.1186/s13059-020-02168-z

The design and construction of reference pangenome graphs with minigraph
Cited 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 rapa
Cited 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 VAriants
Cited by: 25
Author(s): Luca Denti, Marco Previtali, Giulia Bernardini, Alexander Schönhuth, Paola Bonizzoni
Software Mentions: 1
Published: over 5 years ago

Ecosyste.ms: Papers

Projects: pypi: vg

Papers Mentioning vg 34