1. Introduction


Alta-Cyclic is an improved Solexa (Illumina) base caller that gives more accurate base calls. It learns the specific noise pattern in the run, and finds near-optimal parameters to call the base from the noise. We successfully improved reads from both GAI and GAII machines. On the GAI platform we could obtain valuable information after 50 cycles, and from the GAII, we could obtain valuable information after 78 cycles.


2. Installing Alta-Cyclic


Alta-Cyclic package needs the following components on the cluster:

  1. Perl interpreter (we tested it under perl 5.8.8).
  2. C compiler (gcc)
  3. GNU scientific library (gsl)
  4. Sun Grid Engine (SGE)
  5. Blat
  6. libSVM
  7. gzip and gunzip
  8. The following Perl modules:

·  Readonly

·  Storable

·  Carp

·  PDL

·  PDL::Complex


·  Benchmark

·  Data::Dumper

·  Time::HiRes

·  List::Util

·  File::Temp

·  Getopt::Long

·  Archive::Tar

·  Cwd

·  File::Copy

·  Fie::Basename

·  FindBin

·  Hash::Util

·  List::MoreUtils


·  Term::ANSIColor

·  FILE::Glob

·  Term::ReadKey

·  Time::Local

·  Time::Localtime

·  POD::Usage

·  LWP


3. Using Alta-Cyclic




4. Frequently Asked Questions (FAQ)



What is Alta-Cyclic?

            Alta-Cyclic is a novel Solexa base caller that allows more accurate and longer reads.

How are you?

            Alta-Cyclic was developed by a group of scientists from Cold Spring Harbor Laboratory.

What is the difference between Alta-Cyclic and Solexa pipeline?


What is Alta-Cyclic’s license?

            Alta-Cyclic is available free for academic, non-profit and personal use. See license here


I am not falling in the category of the license?

            Please contact us for licensing information.


How do I cite Alta-Cyclic?



Sequencing Technology


How does Alta-Cyclic work?

            Alta-Cyclic takes a trainings library and finds the optimal parameters to extract the signal from the noise. We found that there are three sources of noise in Solexa sequencing that disrupt the signal in later cycles: nascent strand length spread (AKA phasing), fading, and changes in the fluorophores cross talk. In particular, we built a mathematical model that describes the length spread,


Alta-Cyclic can reduce the affect of these noise sources. It uses iterative grid search to find the best para


Where can I get an introduction to Solexa sequencing?


Where can I get more information about your mathematical model?


Does Alta-Cyclic report quality scores?


Does the GC content of the called library affect the training session?





What is the training library?


What is the trim option?






I don’t have a computer cluster, can I get a stand alone version?

No, unfortunately. Alta-Cyclic uses extensive calculations that will make any stand alone version worthless.

I do have computer cluster, can I work on other submission system than Sun Grid Engine (SGE)?

Not with this current version. See ‘Developing with Alta-Cyclic’ for more details how Alta-Cyclic uses SGE.

What are Alta-Cyclic dependencies?


Developing with Alta-Cyclic