- Illumina NGS basics (firm up what clusters and PHRED scores are)
- basic Linux commands, command line structure
- FastQC recap
- PHRED scores and their encoding (aka what is
phred33
?) - File permissions (aka why are the
EGL*.fastq
files and theNZ*.fastq
files shown in different colours?) - Intro into
bash
program control flow and I/O redirection (aka how does thatwhile read name do reads_first.py ... done < namelist.txt
thing work?) - alignments, multiple alignments
- processes (and threads), multiprocessing (aka what's this GNU
parallel
thing?) - principles / heuristics / tips and tricks / hacks ... and how to distinguish these
- Software Carpentry provide a lesson on The Unix Shell which can be used for self-paced study.
Please send suggestions to me at jttkim@gmail.com or j.kim@kew.org