Here we present an ultra-fast computational pipeline BPGA (Bacterial Pan Genome Analysis tool) with seven functional modules. In addition to the routine pan genome analyses, BPGA introduces a number of novel features for downstream analyses like core/pan/MLST (Multi Locus Sequence Typing) phylogeny...
Analysis based on comprehensive core genes should thus serve as a powerful profiling tool to better understand major constituents in fermented food microbiomes.doi:10.1038/s41598-017-11385-9Kim, YihwanKoh, InSongYoung Lim, MiChung, Won-Hyong...
PanPhlAn [31] is a tool that focuses on identifying the genetic composition of individual strains from metagenomes. This tool can characterize pan-genome and metagenome at the strain level, and determine the taxonomic profile, strain-level profile, functional profile, and phylogenetic profile from ...
地址： http://pgaweb.vlcc.cn/ PGAP本地： https://sourceforge.net/projects/pgap/ PGAP: pan-genomes analysis pipeline.Bioinformatics,2012 被引：328 PanGP: a tool for quickly analyzing bacterial pan-genome profile.Bioinformatics,2014 被引：95 PGAP-X: Extension on pan-g...
Multiple may be entered, seperated by a comma [default: CDS] -n|--nucl CDS are not translated to AA sequence [default: off] --pan-opt additional arguments to pass to pangenome_contruction --pan-off don't run pangenome tool [assumes PIRATE has been previously run and resulting files ...
4.3Bioinformatics tools to determine pan-genome Various tools have been developed forpan-genomeanalysis. EDGAR, a web-tool software can be used that performs homology analyses based on a defined threshold value that is automatically adjusted to the query data[54]. The orthology analysis to calculate...
Note: if you are using the step by step interface instead of cactus-graphmap-join, make sure to pass the same --reference options to each tool!PipelineThe Minigraph-Cactus pipeline is run via the cactus-pangenome command. It consists of five stages which can also be run individually (...
12.Wang, Y. et al. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Res. 40, e49 (2012). 13.Haas, B. J. et al. DAGchainer: a tool for mining segmental ...
we reported a tool EUPAN [22] based on a “map-to-pan” strategy and applied it to more than 3000 rice genomes [13]. Nevertheless, due to the large size of the human genome, EUPAN cannot be applied for human pan-genome analysis because of the huge memory size requirement of the de...
The reliance on a solitary linear reference genome has imposed a significant constraint on our comprehensive understanding of genetic variation in animals. This constraint is particularly pronounced for non-reference sequences (NRSs), which have not been