Read Names for Paired-End Reads

By a common convention, read names can include suffixes (such as /1 or /2), which indicate the end of a pair the read represents. For BAM input using the --pair-by-name option, DRAGEN ignores these suffixes to find matching pair names. By default, DRAGEN uses the forward slash character as the delimiter for these suffixes and ignores the /1 and /2 when comparing names. By default, DRAGEN strips these suffixes from the original read names.

DRAGEN provides the following options to control how suffixes are used:

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To change the delimiter character for suffixes, use the --pair-suffix-delimiter option. Valid values for this option include forward-slash (/), dot (.), and colon (:).

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To preserve the entire name, including the suffixes, set --strip-input-qname-suffixes to false.

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To append a new set of suffixes to all read names, set --append-read-index-to-name to true, where the delimiter is determined by the --pair-suffix-delimiter option. By default the delimiter is a slash, so /1 and /2 are added to the names.