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.
Alta-Cyclic package needs the following components on the cluster:
· Readonly
· Storable
· Carp
· PDL
· PDL::Complex
· PDL::FFT
· Benchmark
· Data::Dumper
· Time::HiRes
· List::Util
· File::Temp
· Getopt::Long
· Archive::Tar
· Cwd
· File::Copy
· Fie::Basename
· FindBin
· Hash::Util
· List::MoreUtils
· POSIX
· Term::ANSIColor
· FILE::Glob
· Term::ReadKey
· Time::Local
· Time::Localtime
· POD::Usage
· LWP
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?
T
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?
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?