Wednesday, March 6, 2013

command line reverse complement sequence in linux shell

Sometimes it seems like BSD / GNU / Linux folks thought of everything.

echo AATGATACGGCGACCACCGG | rev | tr ATGC TACG

I'm a bowtie2 partisan too

I mean, I totally agree with the conclusions, but, um, is there a conflict of interest here?  Just sayin.



"... Our results clearly showed the significant reduction in memory footprint and runtime provided by FM-index based aligners at a precision and recall comparable to the best hash table based aligners. Furthermore, the recently developed Bowtie 2 alignment algorithm shows a remarkable tolerance to both sequencing errors and indels, thus, essentially making hash-based aligners obsolete."

Citation: Lindner R, Friedel CC (2012) A Comprehensive Evaluation of Alignment Algorithms in the Context of RNA-Seq. PLoS ONE 7(12): e52403. doi:10.1371/journal.pone.0052403
Editor: Steven L. Salzberg, Johns Hopkins University, United States of America
Received: August 30, 2012; Accepted: November 16, 2012; Published: December 26, 2012