Part II project (Natural Sciences undergrad) under Department of Biochemistry, University of Cambridge; Supervised by Rui Guan and Kiran Patil
The pipeline runs in the following steps. Some shell scripts were written to run all samples in bulk.
00.data Raw sequencing data of parental strains, chemical-evolved strains, and water-control strains.
01.filter Use fastq to filter raw data See more https://github.com/OpenGene/fastp
02.call_variants Install and test snippy and breseq to call variants. Modified the snippy package by diverting towards re_filter_raw_vcf.sh, for project-specific usage.
03.data_analysis Data handled using R.