<p>Hi,</p>

<p>Imagine a Fastq file generated from a Roche 454 platform. You have no information whatsoever about the protocol that what used. The header of the reads give no specific information, just random alphanumeric characters. Each read starts with a 30 bp sequence and ends with a 15bp sequence that look to me like an adapter (?).</p>

<p>How can I be sure that reads are single-ends or paired-ends? Is there anyway to know that just on the basis of sequence information?</p>

<p>Thanks ;)</p>

For 454 flx:

    grep 'GTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTCGGTTCCAAC' 454Reads.fastq | wc -l

You should see a big number for 454 'paired-end' data, or 0 for single end data.

The built-in linker sequences are:

1. -linker flx -- GTTGGAACCGAAAGGGTTTGAATTCAAACCCTTTCGGTTCCAAC, a palindrome, equal to its own reverse complement.
2. -linker titanium -- TCGTATAACTTCGTATAATGTATGCTATACGAAGTTATTACG and the reverse-complement CGTAATAACTTCGTATAGCATACATTATACGAAGTTATACGA.

For more, <a href="http://wgs-assembler.sourceforge.net/wiki/index.php/SffToCA">http://wgs-assembler.sourceforge.net/wiki/index.php/SffToCA</a>