Efficient sequence analysis with bqtools
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Grep - Paired

Note that we may actually be interested in searching for the pattern in only one sequence of a record. By default, bqtools grep will search for the patterns provided in both sequences of a record and return the record if it matches the pattern in either sequence.

We can limit our search to just the primary (R1) sequence by providing a pattern to the -r/--reg1 flag or limit to just the extended (R2) sequence by providing a pattern to the -R/--reg2 flag.

Let’s test this out and find records that have the pattern GGGG in the primary sequence and TTTTACGT in the extended sequence.

bqtools grep merged.vbq -r GGGG -R TTTTACGT

Well that’s not very many! How many exactly? Well let’s count them!

bqtools grep merged.vbq -r GGGG -R TTTTACGT -C
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