Published August 30, 2023
| Version 1.0
Software
Open
LOCLA: Local Optimization for Chromosome-Level Assembly
Authors/Creators
- 1. Institute of Information Science, Academia Sinica, Taipei, 115, TAIWAN
- 2. Ocean Data Bank, Institute of Oceanography, National Taiwan University, Taipei, TAIWAN
- 3. TMU Research Center of Cancer Translational Medicine, Taipei Medical University, Taipei, TAIWAN
Description
LOCLA is a novel genome assembly optimization tool, LOCLA, that iteratively enhances the quality of an assembly by locating sequencing reads on partially assembled scaffolds and thus enable gap filling and further scaffolding. LOCLA utilizes reads of diverse sequencing techniques, e.g., 10x Genomics (10xG) Linked-Reads, PacBio HiFi Reads and Oxford Nanopore Technologies. In our own experiments, we assembled 10x Genomics (10xG) Linked-Reads via Supernova assembler and TGS reads via Canu. Additional tools incorporated in our pipeline include Hybrid Scaffold developed by Bionano Genomics and RagTag.
Notes
The docker image of LOCLA is freely accessible at https://hub.docker.com/r/lsbnb/locla . Usage and technical notes are provided at our Githib website: https://github.com/lsbnb/locla .