[ fxtools trim ]

Summary

This tool can be used to select and trim sequences that contain a specified adapter sequence.

This can almost be thought of as a combination of grep and sed, where everything before the grep match is removed.

By default the adapter sequence is kept (the adapter will be a common prefix for all kept reads) but it can also be trimmed away.

Usage

# trim away sequences prefixing the adapter
fxtools trim -i <your_seq.fq.gz> -a ACTTGGA

# trim away sequences prefixing the adapter + the adapter
fxtools trim -i <your_seq.fq.gz> -a ACTTGGA --trim-adapter