NAME

       fastaq_sequence_trim  -  Trim  exact  matches  to  a  given  string off the start of every
       sequence

DESCRIPTION

       usage:  fastaq_sequence_trim  [options]  <infile_1>  <infile_2>  <outfile_1>   <outfile_2>
       <trim_seqs>

       Trims sequences off the start of all sequences in a pair of sequence files, whenever there
       is a perfect match. Only keeps a read pair if both reads  of  the  pair  are  at  least  a
       minimum length after any trimming

   positional arguments:
       infile_1
              Name of forward fasta/q file to be trimmed

       infile_2
              Name of reverse fasta/q file to be trimmed

       outfile_1
              Name of output forward fasta/q file

       outfile_2
              Name of output reverse fasta/q file

       trim_seqs
              Name of file of sequences to search for at the start of each input sequence

   optional arguments:
       -h, --help
              show this help message and exit

       --min_length INT
              Minimum length of output sequences [50]

       --revcomp
              Trim  the end of each sequence if it matches the reverse complement. This option is
              intended for PCR primer trimming