When using Ion Torrent data, the mergeIonTorrentShortReads command causes overlapping short reads to merge into mini-contigs.

Parameter Description Allowed values
output (required) Specifies the path and directory of the output files. [directory/filename enclosed in quotes]
query (required) Specifies the directory and file name(s) of the query data to be assembled. A folder with one or data files can also be used in place of individual file names. [directory/filename enclosed in quotes]

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