Chimeras In 454 Sequences

Question

[Monzoor]

Do chimeras form occur only in 16S sequences ? Is there a possibility that 454 reads generated from environmental samples (metagenomics data sets using WGS approach) also contain chimeras.

Are chimeras restricted to only 16s sequence data? If yes? Why?

[Monzoor]

Are there bioinformatics programs available that will enable the identification of chimeras in non-16S samples ? Will existing programs (suited for 16S chimeras) identify these artifacts ?

Answer 1

[Pawel Szczesny]

Chimeras are products of amplification - you will find chimeras in any sample that has been amplified by PCR before sequencing (here you have a paper dealing with chimeras in ultra-deep sequencing of mixed viral populations). In 16S rRNA it just occurs more often because the gene is highly conserved.

See more - http://www.bioinformatics-toolkit.org/Help/Topics/chimera.html

Answer 2

[Jake]

Have you checked out the AmpliconNoise pipeline (Perseus) http://code.google.com/p/ampliconnoise/downloads/list?

There is also the Qiime ChimeraSlayer pipeline http://qiime.sourceforge.net/tutorials/chimera_checking.html

Answer 3

[Marina Manrique]

I'd like to point out that most of the time the 16S amplicon sequences are covered in single reads so no assembly is needed prior to the bacterial identification. This is good because chimeras due to misassemblies don't occur.