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References from Revisiting pangenome openness with k-mers. Local targets link to admitted publications; unresolved targets remain external evidence.
A global reference for human genetic variation
10.1038/nature15393 · 2015 · External reference
PANINI: Pangenome Neighbour Identification for Bacterial Populations
10.1099/mgen.0.000220 · 2019 · External reference
Coagulase-Negative Staphylococci Pathogenomics
10.3390/ijms20051215 · 2019 · External reference
Comparative genomic analysis of Staphylococcus lugdunensis shows a closed pan-genome and multiple barriers to horizontal gene transfer
10.1186/s12864-018-4978-1 · 2018 · External reference
Comparative genome-scale modelling of <span class="italique">Staphylococcus aureus</span> strains identifies strain-specific metabolic capabilities linked to pathogenicity
10.1073/pnas.1523199113 · 2016 · External reference
PGAT: a multistrain analysis resource for microbial genomes
10.1093/bioinformatics/btr418 · 2011 · External reference
Heaps’ Law and Heaps functions in tagged texts: evidences of their linguistic relevance
10.1098/rsos.200008 · 2020 · External reference
BPGA- an ultra-fast pan-genome analysis pipeline
10.1038/srep24373 · 2016 · External reference
Haplotype-resolved de novo assembly using phased assembly graphs with hifiasm
10.1038/s41592-020-01056-5 · 2021 · External reference
PanACEA: a bioinformatics tool for the exploration and visualization of bacterial pan-chromosomes
10.1186/s12859-018-2250-y · 2018 · External reference
Power-Law Distributions in Empirical Data
10.1137/070710111 · 2009 · External reference
How to apply de Bruijn graphs to genome assembly
10.1038/nbt.2023 · 2011 · External reference
Genome and Evolution of Yersinia pestis
10.1007/978-94-024-0890-4_6 · 2016 · External reference
Prokaryote pangenomes are dynamic entities
10.1016/j.mib.2022.01.005 · 2022 · External reference
panX: pan-genome analysis and exploration
10.1093/nar/gkx977 · 2017 · External reference
Search and clustering orders of magnitude faster than BLAST
10.1093/bioinformatics/btq461 · 2010 · External reference
An efficient algorithm for large-scale detection of protein families
10.1093/nar/30.7.1575 · 2002 · External reference
PanOCT: automated clustering of orthologs using conserved gene neighborhood for pan-genomic analysis of bacterial strains and closely related species
10.1093/nar/gks757 · 2012 · External reference
CD-HIT: accelerated for clustering the next-generation sequencing data
10.1093/bioinformatics/bts565 · 2012 · External reference
PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph
10.1371/journal.pcbi.1007732 · 2020 · External reference
Unresolved reference
1978 · External reference
Explicit Calculation of the Rarefaction Diversity Measurement and the Determination of Sufficient Sample Size
10.2307/1934716 · 1975 · External reference
Faster method for estimating the openness of species
10.24072/pci.mcb.100185 · 2024 · External reference
KMC 3: counting and manipulating <span class="italique">k</span>-mer statistics
10.1093/bioinformatics/btx304 · 2017 · External reference
OrthoMCL: Identification of Ortholog Groups for Eukaryotic Genomes
10.1101/gr.1224503 · 2003 · External reference
Functional Profiling and Evolutionary Analysis of a Marine Microalgal Virus Pangenome
10.3390/v15051116 · 2023 · External reference
A fast, lock-free approach for efficient parallel counting of occurrences of <span class="italique">k</span>-mers
10.1093/bioinformatics/btr011 · 2011 · External reference
Roary: rapid large-scale prokaryote pan genome analysis
10.1093/bioinformatics/btv421 · 2015 · External reference
lucaparmigiani/Pangenome-Openness: Pangenome- Openness. Version v1.0.0.
10.5281/zenodo.8256094 · 2023 · External reference
Supplementary Material – Revisiting pangenome openness with k-mers
10.5281/zenodo.8233908 · 2023 · External reference
The large-scale blast score ratio (LS-BSR) pipeline: a method to rapidly compare genetic content between bacterial genomes
10.7717/peerj.332 · 2014 · External reference
Prokka: rapid prokaryotic genome annotation
10.1093/bioinformatics/btu153 · 2014 · External reference
PanTools: representation, storage and exploration of pan-genomic data
10.1093/bioinformatics/btw455 · 2016 · External reference
Efficient inference of homologs in large eukaryotic pan-proteomes
10.1186/s12859-018-2362-4 · 2018 · External reference
micropan: an R-package for microbial pan-genomics
10.1186/s12859-015-0517-0 · 2015 · External reference
Genome analysis of multiple pathogenic isolates of <span class="italique">Streptococcus agalactiae</span>: Implications for the microbial “pan-genome”
10.1073/pnas.0506758102 · 2005 · External reference
Comparative genomics: the bacterial pan-genome
10.1016/j.mib.2008.09.006 · 2008 · External reference
Computational pan-genomics: status, promises and challenges
10.1093/bib/bbw089 · 2016 · External reference
Robust analysis of prokaryotic pangenome gene gain and loss rates with Panstripe
10.1101/gr.277340.122 · 2023 · External reference
A Review of Pangenome Tools and Recent Studies
10.1007/978-3-030-38281-0_4 · 2020 · External reference
Kraken: ultrafast metagenomic sequence classification using exact alignments
10.1186/gb-2014-15-3-r46 · 2014 · External reference
Accelerating read mapping with FastHASH
10.1186/1471-2164-14-s1-s13 · 2013 · External reference
PanGP: A tool for quickly analyzing bacterial pan-genome profile
10.1093/bioinformatics/btu017 · 2014 · External reference
PGAP: pan-genomes analysis pipeline
10.1093/bioinformatics/btr655 · 2011 · External reference