SUMMARY: Parallel visualization of multiple individual human genomes is a complex endeavor that is rapidly gaining importance with the increasing number of personal, phased and cancer genomes that are being generated. It requires the display of variants such as SNPs, indels and structural variants that are unique to specific genomes and the introduction of multiple overlapping gaps in the reference sequence. Here, we describe GenPlay Multi-Genome, an application specifically written to visualize and analyze multiple human genomes in parallel. GenPlay Multi-Genome is ideally suited for the comparison of allele-specific expression and functional genomic data obtained from multiple phased genomes in a graphical interface with access to multiple-track operation. It also allows the analysis of data that have been aligned to custom genomes rather than to a standard reference and can be used as a variant calling format file browser and as a tool to compare different genome assembly, such as hg19 and hg38. AVAILABILITY AND IMPLEMENTATION: GenPlay is available under the GNU public license (GPL-3) from http://genplay.einstein.yu.edu. The source code is available at https://github.com/JulienLajugie/GenPlay.
SUMMARY: Parallel visualization of multiple individual human genomes is a complex endeavor that is rapidly gaining importance with the increasing number of personal, phased and cancer genomes that are being generated. It requires the display of variants such as SNPs, indels and structural variants that are unique to specific genomes and the introduction of multiple overlapping gaps in the reference sequence. Here, we describe GenPlay Multi-Genome, an application specifically written to visualize and analyze multiple human genomes in parallel. GenPlay Multi-Genome is ideally suited for the comparison of allele-specific expression and functional genomic data obtained from multiple phased genomes in a graphical interface with access to multiple-track operation. It also allows the analysis of data that have been aligned to custom genomes rather than to a standard reference and can be used as a variant calling format file browser and as a tool to compare different genome assembly, such as hg19 and hg38. AVAILABILITY AND IMPLEMENTATION: GenPlay is available under the GNU public license (GPL-3) from http://genplay.einstein.yu.edu. The source code is available at https://github.com/JulienLajugie/GenPlay.
Authors: Mathieu Blanchette; W James Kent; Cathy Riemer; Laura Elnitski; Arian F A Smit; Krishna M Roskin; Robert Baertsch; Kate Rosenbloom; Hiram Clawson; Eric D Green; David Haussler; Webb Miller Journal: Genome Res Date: 2004-04 Impact factor: 9.043
Authors: Jared C Roach; Gustavo Glusman; Arian F A Smit; Chad D Huff; Robert Hubley; Paul T Shannon; Lee Rowen; Krishna P Pant; Nathan Goodman; Michael Bamshad; Jay Shendure; Radoje Drmanac; Lynn B Jorde; Leroy Hood; David J Galas Journal: Science Date: 2010-03-10 Impact factor: 47.728
Authors: Daniel Blankenberg; Gregory Von Kuster; Nathaniel Coraor; Guruprasad Ananda; Ross Lazarus; Mary Mangan; Anton Nekrutenko; James Taylor Journal: Curr Protoc Mol Biol Date: 2010-01
Authors: Jacob O Kitzman; Alexandra P Mackenzie; Andrew Adey; Joseph B Hiatt; Rupali P Patwardhan; Peter H Sudmant; Sarah B Ng; Can Alkan; Ruolan Qiu; Evan E Eichler; Jay Shendure Journal: Nat Biotechnol Date: 2010-12-19 Impact factor: 54.908