Difference between revisions of "General Statistical Calculation Tool"
From GcatWiki
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=Features= | =Features= | ||
| − | ==Calculate Distribution of Read Lengths== | + | ===Calculate Distribution of Read Lengths=== |
==Calculate How Many Substrings== | ==Calculate How Many Substrings== | ||
*http://genometools.org/index.html - for both k-mer calculation tool and substring tool | *http://genometools.org/index.html - for both k-mer calculation tool and substring tool | ||
Revision as of 19:32, 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
- http://code.google.com/p/biopieces/wiki/calc_N50 - part of biopieces
- Perl Script - and step by step idea
- Python code
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
- People skeptical of this method http://seqanswers.com/forums/showthread.php?t=10988
- Other Method - http://www.cmb.usc.edu/papers/msw_papers/msw-149.pdf
Motivation
http://phagesdb.org/sort/ - it looks like genome size and gc% roughly correlates to the phage cluster
