fastaq-sequence_trim

FASTAQ-SEQUENCE_TRIM(1)          User Commands         FASTAQ-SEQUENCE_TRIM(1)



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



fastaq 3.17.0                      July 2018           FASTAQ-SEQUENCE_TRIM(1)