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Adapters Vs Pcr Fragments

Hi,

I found the belowfew software to remove adapters:

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.

markduplicates pcr adaptor illumina
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updated by Istvan Albert Istvan Albert • written by ric • ric

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

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written by Istvan Albert Istvan Albert

1 answer

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.

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written by Istvan Albert Istvan Albert

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

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written by ric • ric

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

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written by Istvan Albert Istvan Albert

What kind of terms would you recommend:

  • for SNP discovery
  • assembly

Thank you in advance.

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written by ric • ric

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