RS_ReadsOfInsert_Mapping Protocol

Use this protocol to generate consensus sequences from single molecules.

• Note: This protocol replaces the RS_Resequencing_ReadsOfInsert protocol in previous releases.

• Filters reads, maps them to a provided reference sequence, and then identifies consensus and variants against this reference.

• Haploid variants and small indels, but not diploid variants, are called during consensus.

Filtering Parameters (Reads Of Insert)

• Minimum Full Passes: The minimum number of full-length passes over the insert DNA for the read to be emitted.
• Minimum Predicted Accuracy: The minimum predicted accuracy (in %) of the reads of insert emitted.
• Minimum Length of Reads of Insert (In Bases): Reads of insert shorter than this value (in base pairs) are filtered out and excluded from analysis.
• Maximum Length of Reads of Insert  (In Bases): Reads of insert longer than this value (in base pairs) are filtered out and excluded from analysis.

Mapping Parameters (BLASR RoI v1)

• Maximum Divergence (%): The maximum allowed divergence (in %) of a read from the reference sequence.
• Minimum Anchor Size: The minimum size of the read (in base pairs) that must match against the reference sequence.
• Write Output as a BAM File: Specify whether or not to output a BAM representation of the cmp.h5 file.
• Write BED Coverage File: Specify whether or not to output a BED representation of the depth of coverage summary.
• Place Repeats Randomly: Specify that if BLASR maps a read to more than one location with equal probability, then it randomly selects which location it chooses as the best location. If not set, BLASR defaults to the first on the list of matches.