Adapters Vs Pcr Fragments

Question

[ric]

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.

[Istvan Albert]

by the way, this is a nice collection of tools listed here

Answer 1

[Istvan Albert]

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.

[ric]

Thank you. What kind of software would you recommend for each term?

[Istvan Albert]

you a have a good list to start with - remember there is no single best tool - the right answer depends on many factors, most importantly what are you able to run in the first place

[ric]

What kind of terms would you recommend:

• for SNP discovery
• assembly

Thank you in advance.