fastq-join - ea-utils: join two paired-end reads on the overlapping ends
] <read1.fq> <read2.fq>
] -o <read.%.fq>
fastq-join: invalid option --
'h' Unknown option `-h'.
Joins two paired-end reads on the overlapping ends.
FIL See 'Output' below -v
C Verifies that the 2 files probe
id's match up to char C
- use ' ' (space) for Illumina reads
N N-percent maximum difference (8) -m
N N-minimum overlap (6)
FIL Verbose stitch length report -R
No reverse complement
Allow insert < read length
- You can supply 3 -o arguments, for un1, un2, join
files, or one
argument as a file name template. The suffix 'un1, un2, or join' is appended to
the file, or they replace a %-character if present.
- If a 'mate' input file is present (barcode read), then the
'un3' and 'join2' are also created.