Difference between revisions of "General Statistical Calculation Tool"
From GcatWiki
(→Calculate N50) |
(→Calculate N50) |
||
| Line 9: | Line 9: | ||
*http://code.google.com/p/biopieces/wiki/calc_N50 - part of biopieces | *http://code.google.com/p/biopieces/wiki/calc_N50 - part of biopieces | ||
*[http://genomics-array.blogspot.com/2011/02/calculating-n50-of-contig-assembly-file.html Perl Script] - and step by step idea | *[http://genomics-array.blogspot.com/2011/02/calculating-n50-of-contig-assembly-file.html Perl Script] - and step by step idea | ||
| + | *[http://seqanswers.com/forums/showthread.php?t=2857 Python code] | ||
==Calculate GC Content== | ==Calculate GC Content== | ||
Revision as of 16:03, 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
