arahuja/bdg-sparkbench

Benchmarks for Genomics on Spark

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bdg-sparkbench

Benchmarks for Genomics on Spark

Reference Statistics

Downloading a reference genome

wget ftp://[email protected]/bundle/2.8/hg19/ucsc.hg19.fasta.gz

Generating reference stats

spark-submit 
  --num-executors 100 
  --executor-memory 4g 
  --class org.hammerlab.sparkbench.ReferenceStatistics 
  --properties-file spark.conf 
  target/bdg-sparkbench-with-dependencies-0.1-SNAPSHOT.jar 
    --reference ucsc.hg19.fasta
    --substringLength 30 
    --outputPath hg19-reference-stats 
    --sort

Contributors

arahuja

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