Hi,

I found the belowfew software to remove adapters:

• TagDust - eliminate artifactual sequence from NGS data http://www.biomedcentral.com/1471-2164/12/382 http://bioinformatics.oxfordjournals.org/content/25/21/2839.full
• FAR: http://sourceforge.net/apps/mediawiki/theflexibleadap/index.php? title=Main_Page
• Trimmomatic: http://www.usadellab.org/cms/index.php?page=trimmomatic
• http://code.google.com/p/cutadapt/
• https://github.com/vsbuffalo/scythe
• http://code.google.com/p/biopieces/wiki/find_adaptor

Adapters the same like PCR fragments?

Running one of the software above would it gives me the same results like MarkDuplicates.jar?

Thank you in advance.

Each of the terms means something different:

• adapter - a known sequence appended to the DNA fragment used either to extend the fragment or tag it in a certain way
• sequencing errors - errors introduced by the sequencing instrument
• PCR artifacts - artificial sequences that are caused by the PCR amplification process
• duplicates - identical sequences that may or may not be cause by error (PCR amplification included)

So you need to pick the software that does what you need.