BAM_Resequencing_Beta Protocol

Use this protocol to map length and quality-filtered reads against a reference sequence, then to identify consensus and variant sequences using the Quiver algorithm.

• This is an experimental version of the RS_Resequencing protocol which uses BAM rather than cmp.h5 as the output file format.
• This protocol is faster than RS_Resequencing for large jobs, but is not yet guaranteed to produce identical results..
• Used for whole-genome or targeted resequencing.

• Filters reads, maps them to a provided reference sequence, and then calls a consensus sequence.

Filtering Parameters (SFilter v1)

• Minimum Subread Length: Subreads shorter than this value (in base pairs) are filtered out and excluded from analysis.
• Minimum Polymerase Read Quality: Polymerase reads with lower quality than this value are filtered out and excluded from analysis.
• Minimum Polymerase Read Length: Polymerase reads shorter than this value (in base pairs) are filtered out and excluded from analysis.

Mapping Parameters (BLASR v1)

• Maximum Divergence (%): The maximum allowed divergence 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.
• 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.

Consensus Parameters (Quiver v1)

• Use Only Unambiguously Mapped Reads: Specify whether or not to filter out reads where Map QV is less than 10. This reduces coverage in repeat regions that are shorter than the read length.