Options for clc_sort_pairs
usage: clc_sort_pairs [options]
Split SOLiD and Ion Torrent mate pair and paired end sequence files according to
their names to produce a file with paired sequences and one with unpaired sequences.
For SOLiD mate pair input the pairs in the paired output file will have R3 sequence
first and F5 sequence last. For SOLiD paired end input the pairs in the paired output
file will have F3 sequence first and F5 sequence last.
For Ion Torrent input the pairs in the paired output file will consist of a sequence
from the first input file as the first sequence and a sequence from the second input
file as the last sequence.
Options:
-h / --help: Display this help
-i <file1> <file2> / --input <file1> <file2>: Input files, either mate pair files
or paired end files
-q <file1> <file2> / --quality <file1> <file2>: Specify two input quality files.
-s <file> / --singleoutput <file>: Output fasta or fastq file for single reads
(required)
-p <file> / --pairedoutput <file>: Output fasta or fastq file for paired reads
(required)