Post HybSeq Workshop Session(s)

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 the NZ*.fastq files shown in different colours?)
Intro into bash program control flow and I/O redirection (aka how does that while 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

Recommended Resources

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