Genome Assembly Pipeline

This pipeline is designed to automate the assembly of a genome with the option to perform quality control prior to assembly and allows the user to pick between the MaSuRCa or Unicycler assemblers or the auto option, which will decide choose the assembler for the user based on quality metrics given by Quast.

• Team 1 Genome Assembly
• Software Requirements
• Usage
• References

Team 1- Genome Assembly

The Genome Assembly group members for Team 1 are:

• Cecilia (Hyeonjeong) Cheon
• Devishi Kesar
• Laura Mora
• Lawrence McKinney
• Jessica Mulligan
• Heather Patrick

Software Requirements

1. fastp (if performing read quality assessment and trimming)
2. MaSuRCa (if choosing MaSuRCa or the auto option for performing genome assembly)
3. Unicycler (if choosing Unicycler or the auto option for performing genome assembly)
4. Quast (tool for quality control metrics)

Usage

Update the paths of the tools downloaded from Software Requirements in the config.txt file prior to running the genome assembly pipeline. Note: this pipeline assumes the data is paired end reads and has the naming structure *_1.fq.gz and *_2.fq.gz.

./run_genome_assembly_pipeline.sh [-t <int>] -p <dir_path> -o <dir_name> [-q] -g <m|u|a> [-v] [-h]
    -t    number of threads; default is 4
    -p    path to directory containing gzipped fastq forward and backward reads
    -o    path to output directory
    -q    perform quality control and trimming using fastp
    -g    assembler of choice; can pick between MaSuRCa (m), Unicycler (u), or auto (a) (for auto, pipeline will run both and pick the best option)
    -v    activate verbose mode
    -h    print usage information    

The auto option will pick MaSuRCa as the assembler of choice unless the length is more than 10% shorter than Unicycler.

References

• Shifu Chen, Yanqing Zhou, Yaru Chen, Jia Gu; fastp: an ultra-fast all-in-one FASTQ preprocessor, Bioinformatics, Volume 34, Issue 17, 1 September 2018, Pages i884–i890, https://doi.org/10.1093/bioinformatics/bty560
• Zimin AV, Marçais G, Puiu D, Roberts M, Salzberg SL, Yorke JA. The MaSuRCA genome assembler. Bioinformatics. 2013 Nov 1;29(21):2669-77.
• Wick RR, Judd LM, Gorrie CL, Holt KE (2017) Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Comput Biol 13(6): e1005595. https://doi.org/10.1371/journal.pcbi.100559