Fastidious respiratory Mycoplasma whole genome assembly
A de novo assembly pipeline for Fastidious respiratory Mycoplasma spp. using publicly available open source-tools. It takes in demultiplexed reads from GUPPY and putputs polished de novo assemblies. This pipleline is optomized for Mycoplasma spp. and can be run on most modern Mac or Linux computers. It is possible to use this pipeline with Apple Silicon Macs, either through Rosetta2 or by building the dependencies from source.
Framst, I., C, D. A., Baquero, M., & Maboni, G. (2022). Development of a long-read next generation sequencing workflow for improved characterization of fastidious respiratory mycoplasmas. Microbiology (Reading), 168(11). https://doi.org/10.1099/mic.0.001249
Please also include the following references:
Mikhail Kolmogorov, Jeffrey Yuan, Yu Lin and Pavel Pevzner, "Assembly of Long Error-Prone Reads Using Repeat Graphs", Nature Biotechnology, 2019 https://doi.org/10.1038/s41587-019-0072-8
Li, H. (2021). New strategies to improve minimap2 alignment accuracy. Bioinformatics, 37:4572-4574. https://doi.org/10.1093/bioinformatics/btab705
Vaser, Sovic, I., Nagarajan, N., & Sikic, M. (2017). Fast and accurate de novo genome assembly from long uncorrected reads. Genome Research, 27(5), 737–746. https://doi.org/10.1101/gr.214270.116