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bwa align bioActor

Description

Fast DNA alignment by bwa program.

Execution Choices

  • HadoopMapReduce
  • LocalExecution
  • StratosphereMapReduce

Inputs

querySequenceFileDNA sequence file.
referencePrefixThe prefix of formatted reference database.

Outputs

alignmentFileThe alignment output file in SAM format.

Parameters

programThe command line program to execute.
checkOutputTimestampIf true, verify the last modification timestamp for each output file has increased after execution. If the timestamp has not increased, throw an error.
additionalOptions"bwasw": bwa-sw algorithm is used in fast alignment.
ChoiceThe execution choice to run.

bioKepler is funded by NSF DBI-1062565 under CI Reuse and Advances in Bioinformatics programs. Any opinions, findings and conclusions or recomendations expressed in this material are those of the author(s) and do not necessarily reflect the views of the National Science Foundation (NSF).