Hi folks,
I need a command line trimmer that will handle a seq/qual pair or ab1 file (for sanger reads obviously).
I have tried Lucy and unfortunately, I found:
- it did not trim the resulting sequence, only given the clear range positions in header
-was not aggressive enough in removing low quality, ambiguous and vector contaminants.
I am trying TrimSeq but I am not sure it will do the job (I only want to look fo a specific vector, not a slew of them nor contaminants)
Ideally, you would direct to something like an emboss tool that does what i want quickly.
What do you folks use?
Thanks!
daniel
I need a command line trimmer that will handle a seq/qual pair or ab1 file (for sanger reads obviously).
I have tried Lucy and unfortunately, I found:
- it did not trim the resulting sequence, only given the clear range positions in header
-was not aggressive enough in removing low quality, ambiguous and vector contaminants.
I am trying TrimSeq but I am not sure it will do the job (I only want to look fo a specific vector, not a slew of them nor contaminants)
Ideally, you would direct to something like an emboss tool that does what i want quickly.
What do you folks use?
Thanks!
daniel
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