• GMAP read alignment to reference genome or transcriptome
  • Solexa, 454, SOLiD, Sanger reads
  • Tools for identification and enumeration of nucleotide variants, splice isoforms, and genomic rearrangements
  • Case-control sample comparisons
  • Identification and enumeration of nucleotide variants, splice isoforms, structural variants
  • Search gene/transcript expression
  • Reports sSNPs, nsSNPs, indels, premature stop codons, and splice isoforms. Read coverage statistics are reported by gene or transcript together with a visualization module based upon an individual transcript or genomic segment
  • Result export capability in excel and SAS JMP-Genomics formats

DATA MANAGEMENT Alpheus includes automated database ETL (extract, transfer, and load) tools to import metadata, raw data, and FASTA reads/ quality automatically from the sequencing service.

ANALYSIS PIPELINE The Alpheus pipeline is agnostic as to read type or the sequence library and provides alignment of reads onto reference and sequence variant detection, sequence variant characterization, and statistics reporting. Pipeline characteristics include:

  • Pair-wise alignments use BioJava MegaBLAST and Java GMAP parsers
  • Alignments to reference databases
  • Variant detection (SNPs and indels)

USER INTERFACE AND VISUALIZATION The Alpheus user interface permits the researcher to:

  • Search genes by sequence read criteria
  • View list of candidate genes defined for a project
  • Visualize large data sets in an intuitive manner

NCGR Cyberinfrastructure

The National Center for Genome Resources (NCGR, is known for producing professional quality software tools for bioinformatics research. Alpheus is provided as a software service, meaning that the application is hosted and maintained by NCGR. Our world-class data center provides security and availability for your data.