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http://seqanswers.com/wiki/Software/list
https://wiki.nbic.nl/index.php/Next_Generation_Sequencing:_Software
各種sequence analysis相關的軟體

http://sites.google.com/site/nextgengenomics/ingap
inGAP is an integrated platform for
next-generation sequencing project, the core function of which is to
detect SNPs and indels using a Bayesian algorithm.
(1) It does not
have any read length restriction. It can handle 454 sequencing and/or
Illumina Solexa sequencing and/or Sanger sequencing data sets.
(2)
It can detect most small indels in either single-end or paired-end data
sets. Using the simulated data sets, inGAP could successfully identify
85%-98% of small indels with high accuracy (>99%).
(3) It has a
strong capability to identify variants based on a relatively divergent
reference genome, which bring it to a much wider application other than
resequencing projects.
(4) It provides a user-friendly graphic
interface, through which users can browse, search, check, classify, and
even edit the identified variants.
(5) It can be used to detect
intraspecific polymorphisms (including SNPs and indels) based on a
pairwise comparison of multiple whole genomes.
(6) It employs a global heuristic searching approach to layout contigs based on one or more reference genomes.
(7) It also provides a handful of bioinformatic tools for read simulation, mutation incorporation, format conversion, etc.
(8) inGAP-sv (structural variation detection) will come soon.
•    Installation
inGAP is distributed under the GNU General Public License. The latest version can be downloaded at http://sourceforge.net/projects/ingap/
.
inGAP has been tested on PC, Mac, and Linux systems. To install InGap, type the following commands.
% tar xvfz inGAP_*.tar.gz

•    Demo
We provide a demo for the three applications of inGAP. Please click the "Demo" button.
•    Getting started
1.    Double click the icon “inGAP” at inGAP_HOME or start it from a command line:
% inGAP_HOME/inGAP
or
% java -mx2000m -jar inGAP_HOME/inGAP.jar
Then you will see the following panel: