Software

Software tools for pathogen variation and discovery

READSCAN is a highly scalable parallel program to identify non-host sequences (of potential pathogen origin) and estimate their genome relative abundance in high-throughput sequence datasets. READSCAN accurately classified human and viral sequences on a 20.1 million reads simulated dataset in <27 min using a small Beowulf compute cluster with 16 nodes.

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.‚Äč