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fastaq-sequence_trim - Online in the Cloud

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PROGRAM:

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

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