RS_AHA_Scaffolding Protocol

Use this protocol to build hybrid assemblies up to 200 Mb in size with PacBio reads.

• Improve existing assemblies up to 200 Mb in size by scaffolding with PacBio long reads to join contigs.

• Reads are filtered and assembled with high confidence contigs into scaffolds using a combination of algorithms developed by Pacific Biosciences and the AMOS open-source project.

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.

Assembly Parameters (AHA Long Read v1)

• Parameter Schedule: Defines the number of reads required to link two contigs in the scaffold. High coverage requires several reads, while Low coverage requires a single read.
• Gap Fill: Specify whether or not to fill in gaps with PacBio sequencing data.
• Max Iterations: The maximum number of iterations of overlap-layout-consensus performed by the assembly algorithm.