seqfu interleave
interleave (or ilv) is one of the core subprograms of SeqFu. It's used to produce an interleaved FASTQ file from two separate files containing the forward and the reverse read of a paired-end fragment.
ilv: interleave FASTQ files
Usage: ilv [options] -1 <forward-pair> [-2 <reverse-pair>]
-f --for-tag <tag-1> string identifying forward files [default: auto]
-r --rev-tag <tag-2> string identifying forward files [default: auto]
-o --output <outputfile> save file to <out-file> instead of STDOUT
-c --check enable careful mode (check sequence names and numbers)
-v --verbose print verbose output
-s --strip-comments skip comments
-p --prefix "string" rename sequences (append a progressive number)
guessing second file:
by default <forward-pair> is scanned for _R1. and substitute with _R2.
if this fails, the patterns _1. and _2. are tested.
example:
ilv -1 file_R1.fq > interleaved.fq
What are interleaved files?
Paired end sequences can be stored in two separate files (usually denoted with the _R1 and _R2 strings) or in a single sequence where each sequence pair is stored as two subsequent sequences.
A simple example is depicted below:
=======================================================================
File_R1.fq File_R2.fq Interleaved.fq
=======================================================================
@seq1 @seq1 @seq1
TTTCATTCTGACTGCAACG GGATTAAAAAAAGAGTGTC TTTCATTCTGACTGCAACG
+ + +
IIIIIIIIIIIIIIIIIII IIIIIIIIIIIIIIIIIII IIIIIIIIIIIIIIIIIII
@seq2 @seq2 @seq1
GTGTGGATTAAAAAAAAAA TTTTTTTTTTTTTTTTTTT GGATTAAAAAAAGAGTGTC
+ + +
IIIIIIIIIIIIIIIIIII IIIIIIIIIIIIIIIIIII IIIIIIIIIIIIIIIIIII
@seq3 @seq3 @seq2
AGAGTGTCTGATAGCA GATAGCAG GTGTGGATTAAAAAAAAAA
+ + +
IIIIIIIIIIIIIIII IIIIIIII IIIIIIIIIIIIIIIIIII
@seq2
TTTTTTTTTTTTTTTTTTT
+
IIIIIIIIIIIIIIIIIII
@seq3
AGAGTGTCTGATAGCA
+
IIIIIIIIIIIIIIII
@seq3
GATAGCAG
+
IIIIIIII
Screenshot
