Who are the contaminants in your sequencing project? (crosspost from #microBEnet)

This was originally posted on microBEnet: Who are the contaminants in your sequencing project?

Well, been having many discussions recently about PCR amplification happening from "negative" controls where no sample DNA was added. Such amplification is alas pretty common - due to contamination occurring in some other material added to the PCR reaction.  Obviously it would be best to eliminate all DNA contamination of all reagents and all PCRs.  But if that does not happen, it is possible to try to detect contamination after it has happened.  Below I post some papers related to post-sequencing detection of contamination:

• Common Contaminants in Next-Generation Sequencing That Hinder Discovery of Low-Abundance Microbes.
• Abundant Human DNA Contamination Identified in Non-Primate Genome Databases
• Fast identification and removal of sequence contamination from genomic and metagenomic datasets
• Mycoplasma contamination in the 1000 Genomes Project
• ContEst: estimating cross-contamination of human samples ...
• DeconSeq @ SourceForge.net
• AlienTrimmer: A tool to quickly and accurately trim off ...
• Kraken
• Blobology: exploring raw genome data for contaminants, symbionts, and parasites using taxon-annotated GC-coverage plots

Any other suggestions or comments would be welcome. UPDATE 10:30 AM 7/25 - Was reminded on Twitter of a new, critically relevant publication on this issue: Reagent contamination can critically impact sequence-based microbiome analyses

@pathogenomenick @gregcaporaso crap - can't believe I left that off — Jonathan Eisen (@phylogenomics) July 25, 2014