SVAMP is standalone desktop application to visualise variants (SNPs and indels) and peform realtime analysis on selected regions of a genome on specific samples. SVAMP has some interesting features like phylogeography,allele frequency map and principal coordinate analysis.SVAMP takes VCF files (variant call format) as input. Metainformation on samples are simple tab delimited text files.In addition SVAMP also reads annotation files in GFF format and reference sequences in FASTA format. For more information on SVAMP please see the publication SVAMP: sequence variation analysis, maps and phylogeny.

The software was developed at the Pathogen Genomics Laboratory (PI: Arnab Pain) in KAUST.

1. Download the latest binaries (v 2.10) for your platform from DOWNLOADS section

2. Download the MRSA dataset

3. Unzip the software binary and dataset to a location where the user has permission to create files. Please note that SVAMP creates all temporary files in the same working directory where binary resides.

4. double click on the SVAMP executable to open the application.

5. File->load open the mrsa_science_bundle and TW20_full.fasta,TW20_full.gff,tw20_4310.vcf,tw20.db and click load.

6. Tools->Tree,Tools->PCOA, Tools->Allele Map to visualise the Tree,PCOA plot and allele frequence map.

7. click on the checkbox adjacent to GCdensity,Relative variant density,Fst and Tajima's D tracks to enable the respective graphs.

• Test datasets
  • MRSA dataset from Harris, S.R., et al. (2010) Evolution of MRSA during hospital transmission and intercontinental spread, Science
  • Malaria dataset from Manske, M., et al. (2012) Analysis of Plasmodium falciparum diversity in natural infections by deep sequencing, Nature

• Mac

  SVAMP_2.10.dmg (Right click and select 'Save Link As...')

  SVAMP_2.04.dmg (Right click and select 'Save Link As...')

• Windows

  SVAMP_2.10_win.zip (Right click and select 'Save Link As...')

  SVAMP_2.04_win.zip (Right click and select 'Save Link As...')

• Linux

  SVAMP_2.10_linux_x86_64.zip(Right click and select 'Save Link As...')

  SVAMP_2.04_linux_x86_64.zip(Right click and select 'Save Link As...')

• Source code

  Available on github.com/raeece/svamp

• sample tsv, vcf file and prepare_svamp_bundle.pl script needed to prepare new datsets

  dataset_preparation.zip(Right click and select 'Save Link As...'). For detailed instructions see Manual.

• PCOA
• Phylogenetic tree : circular
  
  
• Phylogenetic tree : non-circular, with selected regions
• Graphs
  
  
• Isolate geographical distribution
  
  
• Map of Allele Frequency Distribution

For download and installation instructions and features see SVAMP manual