This is the command fastaq-sequence_trim that can be run in the OnWorks free hosting provider using one of our multiple free online workstations such as Ubuntu Online, Fedora Online, Windows online emulator or MAC OS online emulator
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
Use fastaq-sequence_trim online using onworks.net services
