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fastaq-sequence_trim - Online in the Cloud

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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

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