\

A switch that makes special characters literal and literal characters special

[]

Character class--used to enclose a list of alternatives

()

Grouping--used to delimit a string comprising a “phrase.” Phrases are necessary in paired end specification so you can match a pair of forward and reverse reads while still distinguishing their orientation. In SeqMan, phrases in parentheses must match for two reads to qualify as a pair; phrases outside the parentheses are used to distinguish members of the same pair.

\d

Any digit (0-9)

\D

Any non-digit character

\w

Any alphanumeric “word” character (including “_”)

.

Any character

|

Alternate--either the term before “|” or after “|”

^

Match at the beginning of the line only

$

Match at the end of the line only