Polishing of genome assemblies

PD Patrick Driguez
SB Salim Bougouffa
KC Karen Carty
AP Alexander Putra
KJ Kamel Jabbari
MR Muppala Reddy
RS Richard Soppe
MC Ming Sin Cheung
YF Yoshinori Fukasawa
LE Luca Ermini
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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] 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].

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