Errata

"This is especially useful if you do occasionally log in with an administrator account with more privileges—the potential risks associated with making a mistake on an account with administrator privileges are much higher, so you should always be away when you’re on this account (and minimize this time as much as possible)."

"away" should be "aware"

"The shell operator && executes subsequent commands only if previous commands have completed with a nonzero exit status:"

Nonzero should be changed to "successful" or "exit code of zero"

The previous sentence indicates "we want to start program2 only after program1 returns a zero (successful) exit code."

"downloading and installing to new Python and R packages" should be "downloading and installing new Python and R packages"

"every table you create should have primary key column" should be

"every table you create should have a primary key column".

Doug McIlory
should be
Doug McIlroy

'Note that you should only use columnt -t to visualize...' -> should this be 'column -t' instead? I don't think columnt is a valid command

organisim() should be organism()

"which is all the more reason to include apply the recommendations below" should be "which is all the more reason to apply the recommendations below"

It should be: The Technical Tools of Statistics (1964) John Tukey and not The Technical Skills of Statistics (1964) John Tukey.

The original text is:

"First, note that some positions such as 215,906,528 and 215,906,528 only contain the alternative allele (in the ALT column) <X>."

Should this be:

"First, note that some positions such as 215,906,528 and 215,906,529 only contain the alternative allele (in the ALT column) <X>."
?

The variable "d" here should be "reps".

"In this cases..." should be reworded to either "In this case..." or "In these/such cases...".

In the final sentence: "...would later make your researcher nearly impossible...", it should say "research" instead of "researcher".

"harddrive" should be "hard drive". This appears twice in this paragraph.

"Others researchers..." should be "Other researchers...".

The final sentence should use "it's/it is crucial" instead of "its crucial".

The final part of the penultimate sentence: "...four times it’s size?" should use "its" instead of "it's". (This is me being a pedant - sorry!)

"If you know a scripting language other than Python like Perl or Ruby, you’ll prepared to follow along most examples..." is presumably missing the word "be", although I think the use of the word "prepared" is a bit awkward here.

"By robust, I mean the your work is..." should read: "By robust, I mean that your work is..."

Text: "Querying information from a set gene models can become quite involved."
s/from a set gene models/from a set of gene models/

The sentence "Working with Git working with these commits"

Maybe should read "When working with Git we use these comments"

The line "Suppose a lab has a clever bioinformatician that writes a script for trims poor quality regions from reads"

I think that "for trims" should read "that trims"