Difference between revisions of "General Statistical Calculation Tool"
From GcatWiki
(→Calculate How Many Substrings) |
(→Calculate How Many Substrings) |
||
| Line 4: | Line 4: | ||
*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 | ||
*[http://adenine.biz.fh-weihenstephan.de/cgi-bin/shustring/shustring.cgi.pl Shustring] (SHortest Unique subSTRING) [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1166540/ paper] | *[http://adenine.biz.fh-weihenstephan.de/cgi-bin/shustring/shustring.cgi.pl Shustring] (SHortest Unique subSTRING) [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1166540/ paper] | ||
| + | *[http://adenine.biz.fh-weihenstephan.de/cgi-bin/shulen/shulen.cgi.pl shulen] - Program for Computing the Null-Distribution of Shortest Unique Substring Lengths in DNA Sequences | ||
==Calculate N50== | ==Calculate N50== | ||
Revision as of 14:46, 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
Motivation
http://phagesdb.org/sort/ - it looks like genome size and gc% roughly correlates to the phage cluster
