pan-genome analysis pipeline (PGAP), which can perform five analytic functions with only one command, including cluster analysis of functional genes, pan-genome profile analysis, genetic variation analysis of f
In this paper, we present a HUman Pan-genome ANalysis (HUPAN) tool and apply it to analyze 275 Han Chinese genomes, including 185 newly sequenced and 90 assembled genomes [23]. HUPAN can also be applied to other eukaryotes with big genome sizes similar to human. Results We have developed...
In this study, we developed a pangenome construction and SV genotype calling pipeline (PSVCP) (Additional file1: Fig. S1). The pipeline includes three main steps, (1) iterative alignment between genomes to identify novel segments, then integrating these sequences into the reference genome to co...
Zhao Y, et al., PGAP: pan-genomes analysis pipeline. Bioinformatics, 2012. 28(3): p. 416-8. Google Scholar [18] C. Laing, et al. Pan-genome sequence analysis using Panseq: an online tool for the rapid analysis of core and accessory genomic regions BMC Bioinf, 11 (2010), p. 461...
Directory structure and analysis output The analysis generates clustering result./data/YourSpecies/allclusters_final.tsv and files required for visualizing the pan-genome usingpan-genome-visualization. ./data YourSpecies # folder specific to the your pan genome - input_GenBank # INPUT: genomes in ...
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-genome analysis pipeline.BMC Genomics,2018 被引：18 PGAweb: A Web Server for ...
Therefore, the present work proposes a new tool called Pan4Drafts, an automated pipeline for pan-genomic analysis of draft prokaryotic genomes to maximize the representation and accuracy of the gene repertoire of unfinished genomes by using reads from sequencing data. Pan4Draft allows to perform ...
The 66 rice genomes were de novo assembled by using a pipeline that combined both the SOAPdenovo2 package (version 2.23)50and the Fermi package (version 1.1)51. Briefly, raw reads were assembled in parallel into contigs by Fermi (run-fermi.pl -Pe) and SOAPdenovo2, and the software Gap...
panX: pan-genome analysis and exploration Nucleic Acids Research(IF16.6)Pub Date : 2017-10-25, DOI:10.1093/nar/gkx977 Wei Ding , Franz Baumdicker , Richard A Neher Horizontal transfer, gene loss, and duplication result in dynamic bacterial genomes shaped by a complex mixture of different mod...
. Classification of accessory segments will be influenced by the diversity of genomes used to build the pangenome. e.g., if all isolates are from a closely related outbreak, a universally present prophage will be classified as core and will be missed by this pipeline. Detection of IS may ...