Its expected that you are familiar all of the following skills/tools. If any of these are new to you, or you’ve only had light exposure in the past, now is the time to brush up by reading the relevant chapters in Bioinformatics Data Skills.
- bash command line
- File manipulation
- grep
- sed
- cut
- find
- less
- piping and redirecting
- tmux
- git
- adding, commiting
- branching, merging, rebasing/squashing
- github: push, pull, fetch
- types of sequence information
- fasta, fai index files
- fastq
- bam/sam
- bed files
- mapping sequencing data with BWA
- sam/bam manipulation with samtools and pysam