Michael Schatz, Ben Langmead, and James Taylor

The goal of this challenge is to identify a viral sequence insertion into a human cancer exome. To keep it tractable, we will only use genes on chromosome 22, and only exons > 500bp long. The subject line should be: BTG2011 human_gene virus_name. The body should contain the steps you took to identify the gene and virus. If at all possible, please include the exact commands used. Winners will be selected by first correct answer (name of gene, name of virus) and for reproducibility. You must be registered and present at Beyond the Genome 2011 to win. The judges decisions are final. Rules are subject to change at anytime.

Download the data here: btg11.tgz

  chr22.fa is the hg19 version of chr22
  read1.fq and read2.fq are the paired end reads from the exome
       (100bp reads, 300bp fragment size, 20x coverage)

Hints

Try assembling the reads (with velvet or SOAPdenovo) and aligning the contigs to the reference genome (with MUMmer or Bowtie2). The insertion will be a segment that doesnt align. You can then BLAST that contig at NCBI to see if it hits any known viruses.

Script for generating the challenge: btg11.sh