flink in bioinfomatics

https://github.com/UDC-GAC/BigDEC

The following command corrects a paired-end dataset using Flink and k-mer length of 15, while merging the output files in HDFS:

flinkrun --args "-p dataset1.fastq dataset2.fastq -k 24 -m file:/output"

flink run "$@" --class es.udc.gac.bigdec.RunEC $BIGDEC_HOME/target/bigdec-bin.jar flink ${BIGDEC_ARGS}

The following command corrects a single-end dataset using Spark and specifies the output directory in HDFS:

sparkrun --args "-s dataset.fastq -o /output"

spark-submit "$@" --class es.udc.gac.bigdec.RunEC $BIGDEC_HOME/target/bigdec-bin.jar spark ${BIGDEC_ARGS}