Cufflinks is a reference-guided assembler for RNA-Seq experiments. It
simultaneously assembles transcripts from reads and estimates their relative
abundances, without using a reference annotation. The software expects as
input RNA-Seq read alignments in SAM format (http://samtools.sourceforge.net).
Here's an example spliced read alignment record:
Primary contact <firstname.lastname@example.org>
Cole Trapnell designed and wrote Cufflinks and Cuffdiff, with substantial technical input
from Geo Pertea, Brian Williams, Ali Mortazavi, Jeltje van Baren, Steven Salzberg, Barbara Wold,
and Lior Pachter. Geo Pertea wrote Cuffcompare. Adam Roberts made substantial improvements to
the abundance estimation model used by Cufflinks and Cuffdiff.
Copyright (C) 2003-2009 Cole Trapnell et al
Boost Software License, Version 1.0
Permission is hereby granted, free of charge, to any person or organization
obtaining a copy of the software and accompanying documentation covered by
this license (t