I need a software which can remove the adaptors in a completely sequenced bacterial genome. The raw fastq was cleaned with Trim_galore, but it seems some adaptors are still in the genome
bbduk, from BBTools:
https://jgi.doe.gov/data-and-tools/bbtools/
You may be able to specify/add and adaptors file
You can use Trimmomatic
http://www.usadellab.org/cms/?page=trimmomatic
You can use Cutadapt to remove specific adapter sequences as you can include the sequence of the adapter of interest that you want to remove in the command as follows:
-a ADAPTER, --adapter=ADAPTER
Sequence of an adapter ligated to the 3' end (paired
data: of the first read). The adapter and subsequent
bases are trimmed.
-g ADAPTER, --front=ADAPTER
Sequence of an adapter ligated to the 5' end (paired
data: of the first read). The adapter and any
preceding bases are trimmed. Partial matches at the 5'
end are allowed.
-b ADAPTER, --anywhere=ADAPTER
Sequence of an adapter that may be ligated to the 5'
or 3' end (paired data: of the first read). Both types
of matches as described under -a und -g are allowed.
If the first base of the read is part of the match,
the behavior is as with -g, otherwise as with -a. This
option is mostly for rescuing failed library
preparations - do not use if you know which end your
adapter was ligated to!
and here's its documentation: https://cutadapt.readthedocs.io/en/stable/
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