Helpful Sequencing Troubleshooting Guide
We have provided a general guide to identifying the common problems that can occur when sequencing DNA on modern DNA sequencers like the ABI 3730 and 3700. This guide offers researcher help for troubleshooting common DNA sequencing problems.
The individual sequencing problem identification and troubleshooting help pages can also be accessed directly from the links below. If you have any questions or comments on these guides we would love to hear from you.
- DNA sequencing troubleshooting help - Failed reactions
- DNA sequencing troubleshooting help - Mixed traces
- DNA sequencing troubleshooting help - Short reads
- DNA sequencing troubleshooting help - Excessive collection times
- DNA sequencing troubleshooting help - Dye blobs
- DNA sequencing troubleshooting help - Noisy traces
- DNA sequencing troubleshooting help - Blurry traces
- DNA sequencing troubleshooting help - Sharp signal spikes
- DNA sequencing troubleshooting help - AT run sequence slippage
- DNA sequencing troubleshooting help - Trace signal hard stops
- DNA sequencing troubleshooting help - Sequencing chemistry breakdown
- DNA sequencing troubleshooting help - Primer dimer formation
- DNA sequencing troubleshooting help - Insertion or deletions (indels)
- DNA sequencing troubleshooting help - Chimeras and sequencing rearrangements
Other DNA Sequencing Service Resources
We have added a forum (Nucleics sequencing forum) where you can ask questions about our products or discuss the best ways to use them. We have also include forums on DNA sequencing where you can ask for help on any sequencing related problems you may be having.
We have written a guide on choosing a DNA sequencing service which provides an overview of the features you should consider when selecting a sequencing service.
Reviews of 143 commercial DNA sequencing services. We have included (where available) information on the following areas: sequencing analysis price, the different sequencing services offered, where the facility is located, DNA template sample requirements, the DNA sequencing instruments used, contact address, phone, fax and email details, and a general comment on the service. The reviews of the individual sequencing services reviewed to date are:
- Agencourt Biosciences DNA sequencing
- Lark Technologies DNA sequencing
- University of Maine DNA sequencing core facility
- SeqWright DNA sequencing
- UCLA DNA sequencing core facility
- GeneWiz DNA sequencing
- Cleveland Genomics
- Commonwealth Biotechnologies
- Tocore DNA sequencing
- Laragen DNA sequencing
- DF/HCC DNA Core Facility
- University of Witwatersrand Core Facility
- Virotech International
- Amplicon Express
- Agowa DNA sequencing
- Polymorphic DNA Technologies
- Sequetech
- Washington University SNP Research Facility
- GATC Biotech DNA sequencing
- Elim Biopharmaceuticals DNA sequencing
- Macrogen DNA sequencing service
- NewLab BioQuality
- Eton Bioscience DNA sequencing
- Lofstrand Labs
- Davis Sequencing
- MTR Scientific
- VBC-BIOTECH Service GmbH
- MCLAB DNA sequencing
- Stony Brook University DNA Core Facility
- Tufts University DNA Core Facility
- Ana-Gen Technologies
- Qiagen DNA Sequencing
- MWG DNA Sequencing
- Northwoods DNA sequencing
- TGen DNA sequencing
- Genemed Synthesis
- Gene Link DNA sequencing
- Gene Gateway sequencing
- DNA LandMarks
- Veritas DNA sequencing
- Functional Biosciences
- STAB VIDA DNA sequencing
- DNA Technologies DNA sequencing
- Vicgene Biotechnology DNA sequencing
- Retrogen DNA sequencing
- Alpha BioLab
- IMGM Laboratories
- SEQLAB DNA sequencing
- BaseClear DNA sequencing
- Eurofins Medigenomix DNA sequencing
- Bionexus sequencing
- University of Cape Town Core Sequencing Facility
- Secugen DNA Sequencing
- DNAmind DNA sequencing
- Microsynth DNA sequencing
- Yale DNA Sequencing Analysis Facility
- Millegen DNA sequencing
- University of Michigan DNA Sequencing Core
- University of Missouri DNA Sequencing Core
Available Nucleics DNA sequencing services, reagents & software resources
Nucleics DNA sequencing software & services home page. Includes recent news about our DNA sequencing services, software & reagents for sequencing DNA.
The PeakTrace DNA Basecaller. This basecaller can improve the read length of all ABI DNA sequencing traces (including the ABI 377) by up to 100%.
We have also added a free version of the PeakTrace basecaller to also allow users to trial the PeakTrace basecaller on their own traces.
The PeakTrace:Box is a freestanding version of the PeakTrace basecaller which allows users to basecall traces within their own facilities without having to upload their sequencing traces to our PeakTrace FTP server.
Recent news from Nucleics about our DNA sequencing products and company. Includes details on recent changes and product releases.
We have added a free online QualTrace version that allows users to test the software on their own traces.
About the history of Nucleics, as well that of the automated sanger DNA sequencing software, reagents & services we offer.
An overview of the software and reagents for sequencing DNA that we offer. This includes the CounterTrace DNA sequencing reagent & software for the phred base caller, the CounterTrace II software & reagent for the DNA, the QualTrace software, the LongTrace DNA sequencing service, the QualTrace ABI trace quality control software, and the dLUTE SEQ DNA sequencing reagent.
An overview of the Genomic & DNA sequencing services that we offer. Includes details on the LongTrace DNA sequencing service as well as on our genome sequencing and bioinformatics services.
Overview of the support Nucleics provides for DNA sequencing troubleshooting and reviews of DNA sequencing service providers. Includes product manuals of guides for our DNA sequencing reagents and software.
How to contacting Nucleics about our DNA sequencing software & reagents. Includes information on our delivery and mailing addresses.
Older news from Nucleics about our DNA sequencing services, software & reagents. Includes reports on our past business activities and successes.
The QualTrace DNA sequencing software for detecting nine different problems with DNA sequencing reactions.
The CounterTrace II DNA sequencing software & DNA sequencing reagent allows users to increase the read length of KB base called sequencing traces by up to 30%.
CounterTrace DNA sequencing reagent and DNA sequencing software designed for use with the ABI 3700 DNA sequencer and phred base caller.
The dLUTE SEQ DNA sequencing reagent allows the BigDye sequencing reagent to be used at amounts equivalent to a 1:320 dilution. This can provide very significant cost savings in large genome sequencing projects.
The dLUTE SEQ CF sequencing premix dilution reagent has been formulated for use by small individual users and core sequencing facilities.
UniSeq DNA sequencing primer library & software
Provides answer to common questions about the UniSeq DNA sequencing system please visit the UniSeq FAQ page.
The full ASIN patent which was sold to Takara Biomedicals in 2000 is now available in html and pdf form.
Our privacy policy is stated on our privacy policy page.
DNA sequencing software & reagent information
CounterTrace II DNA sequencing system overview in pdf format.
QualTrace DNA sequencing software overview in pdf format.
LongTrace DNA sequencing service overview in pdf format.
dLUTE SEQ DNA sequencing mix reagent overview in pdf format.
UniSEQ genome sequencing software & reagent overview in pdf format.
CounterTrace DNA sequencing system overview in pdf format.
UniSeq PCR DNA sequencing FAQ.
Z-Tag protein expression & purification system overview in pdf format.
DNA sequencing software & reagent support
CounterTrace II DNA sequencing software guide.
The dLUTE SEQ BigDye sequencing mix users manual and the dLUTE SEQ users manual in pdf format.
The dLUTE SEQ CF users manual in html and pdf formats.
QualTrace DNA sequencing software users manual.
UniSeq Polymerase Chain Reaction DNA sequencing users manual.
UniFinish sequencing DNA software users manual.
UniSelect genome sequencing software users manual.
CounterTrace DNA sequencing system users manual.
CounterTrace DNA sequencing quick start guide.
CounterTrace DNA sequencing phred base caller integration guide.
CounterTrace II DNA sequencing system Quick Start guide
Material Data Safety Sheets
dLUTE SEQ DNA sequencing reagent MSDS
CounterTrace DNA sequencing loading standard MSDS
UniSeq universal oligonucleotide primer library MSDS
DNA Sequencing Protocols
Advice and protocols for improving sequencing DNA quality
Exonuclease I & SAP PCR clean up
Phenol/Butanol clean up of DNA sequencing reactions