Revision as of 20:34, 8 June 2011

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
• http://www.dolphing.com/?p=508
• 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
• http://www.nature.com/nature/journal/v463/n7279/extref/nature08696-s1.pdf

Motivation

http://phagesdb.org/sort/ - it looks like genome size and gc% roughly correlates to the phage cluster