Difference between revisions of "General Statistical Calculation Tool"
From GcatWiki
(→Calculate How Many Substrings) |
(→Estimate Genome Size) |
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==Estimate Genome Size== | ==Estimate Genome Size== | ||
*http://seqanswers.com/forums/showthread.php?t=11434 | *http://seqanswers.com/forums/showthread.php?t=11434 | ||
| + | *[http://gsizepred.sourceforge.net/ GSP] - incorporate the Bayesian framework and EM algorithm for the genome size prediction | ||
| + | |||
=Motivation= | =Motivation= | ||
http://phagesdb.org/sort/ - it looks like genome size and gc% roughly correlates to the phage cluster | http://phagesdb.org/sort/ - it looks like genome size and gc% roughly correlates to the phage cluster | ||
Revision as of 15:47, 1 June 2011
Contents
Features
Calculate Distribution of Read Lengths
Calculate How Many Substrings
- http://genometools.org/index.html - for both k-mer calculation tool and substring tool
- Shustring (SHortest Unique subSTRING) paper
- Shulen - Program for Computing the Null-Distribution of Shortest Unique Substring Lengths in DNA Sequences
Calculate N50
Calculate GC Content
Calculate k-mer Distributions
- http://genometools.org/index.html - for both k-mer calculation tool and substring tool
- Jellyfish - more recent k-mer counting tool
Estimate Genome Size
- http://seqanswers.com/forums/showthread.php?t=11434
- GSP - incorporate the Bayesian framework and EM algorithm for the genome size prediction
Motivation
http://phagesdb.org/sort/ - it looks like genome size and gc% roughly correlates to the phage cluster
