HiFi Assembly Polishing Pipeline

We polished the CLR-based assemblies using the Arrow algorithm in the gcpp tool from PacBio’s SMRT Link v8.0 stack. First, we aligned the raw CLR data against the initial assembly using pbmm2 v1.1.0, which is a version of Minimap2 [67 (link)] adapted to PacBio’s native format. The alignment is then used for consensus calling and polishing using gcpp v1.0.0. We repeated the process for two additional polishing cycles whereby we feed the polished assembly from the previous cycle as the alignment reference in the next cycle. The HiFi-based assemblies do not require additional polishing to the highly accurate starting CCS sequences [44 (link)].

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Driguez P., Bougouffa S., Carty K., Putra A., Jabbari K., Reddy M., Soppe R., Cheung M.S., Fukasawa Y, & Ermini L. (2021). LeafGo: Leaf to Genome, a quick workflow to produce high-quality de novo plant genomes using long-read sequencing technology. Genome Biology, 22, 256.

Publication 2021

SMRT Link

Smrt

Corresponding Organization :

Other organizations : King Abdullah University of Science and Technology

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Variable analysis

independent variables

Algorithm used for polishing (Arrow algorithm in the gcpp tool)

dependent variables

Polished CLR-based assemblies

control variables

PacBio's SMRT Link v8.0 stack
Pbmm2 v1.1.0 (a version of Minimap2 adapted to PacBio's native format)
Gcpp v1.0.0 for consensus calling and polishing
HiFi-based assemblies (do not require additional polishing)

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