de novo 短序列组装
* MIRA2 - MIRA (Mimicking Intelligent Read Assembly) is able to perform true hybrid de-novo assemblies using reads gathered through 454 sequencing technology (GS20 or GS FLX). Compatible with 454, Solexa and Sanger data. Linux OS required.
* SHARCGS - De novo assembly of short reads. Authors are Dohm JC, Lottaz C, Borodina T and Himmelbauer H. from the Max-Planck-Institute for Molecular Genetics.
* SSAKE - Version 2.0 of SSAKE (23 Oct 2007) can now handle error-rich sequences. Authors are René Warren, Granger Sutton, Steven Jones and Robert Holt from the Canada's Michael Smith Genome Sciences Centre. Perl/Linux.
* VCAKE - De novo assembly of short reads with robust error correction. An improvement on early versions of SSAKE.
* Velvet - Velvet is a de novo genomic assembler specially designed for short read sequencing technologies, such as Solexa or 454. Need about 20-25X coverage and paired reads. Developed by Daniel Zerbino and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI). 

SNP/Indel Discovery
单碱基多态性/插入缺失多态性查找软件

* ssahaSNP - ssahaSNP is a polymorphism detection tool. It detects homozygous SNPs and indels by aligning shotgun reads to the finished genome sequence. Highly repetitive elements are filtered out by ignoring those kmer words with high occurrence numbers. More tuned for ABI Sanger reads. Developers are Adam Spargo and Zemin Ning from the Sanger Centre. Compaq Alpha, Linux-64, Linux-32, Solaris and Mac
* PolyBayesShort - A re-incarnation of the PolyBayes SNP discovery tool developed by Gabor Marth at Washington University. This version is specifically optimized for the analysis of large numbers (millions) of high-throughput next-generation sequencer reads, aligned to whole chromosomes of model organism or mammalian genomes. Developers at Boston College. Linux-64 and Linux-32.
* PyroBayes - PyroBayes is a novel base caller for pyrosequences from the 454 Life Sciences sequencing machines. It was designed to assign more accurate base quality estimates to the 454 pyrosequences. Developers at Boston College. 

Genome Annotation/Genome Browser/Alignment Viewer/Assembly Database
基因组注释/基因组浏览/比对结果浏览/组装数据库

* STADEN - Includes GAP4. GAP5 once completed will handle next-gen sequencing data. A partially implemented test version is available here
* EagleView - An information-rich genome assembler viewer. EagleView can display a dozen different types of information including base quality and flowgram signal. Developers at Boston College.
* XMatchView - A visual tool for analyzing cross_match alignments. Developed by Rene Warren and Steven Jones at Canada's Michael Smith Genome Sciences Centre. Python/Win or Linux.
* SAM - Sequence Assembly Manager. Whole Genome Assembly (WGA) Management and Visualization Tool. It provides a generic platform for manipulating, analyzing and viewing WGA data, regardless of input type. Developers are Rene Warren, Yaron Butterfield, Asim Siddiqui and Steven Jones at Canada's Michael Smith Genome Sciences Centre. MySQL backend and Perl-CGI web-based frontend/Linux. 

ChIP-Seq/BS-Seq

ChIP-Seq / BS-Seq
* FindPeaks - perform analysis of ChIP-Seq experiments. It uses a naive algorithm for identifying regions of high coverage, which represent Chromatin Immunoprecipitation enrichment of sequence fragments, indicating the location of a bound protein of interest. Original algorithm by Matthew Bainbridge, in collaboration with Gordon Robertson. Current code and implementation by Anthony Fejes. Authors are from the Canada's Michael Smith Genome Sciences Centre. JAVA/OS independent. Latest versions available as part of the Vancouver Short Read Analysis Package
* CHiPSeq - Program used by Johnson et al. (2007) in their Science publication
* BS-Seq - The source code and data for the "Shotgun Bisulphite Sequencing of the Arabidopsis Genome Reveals DNA Methylation Patterning" Nature paper by Cokus et al. (Steve Jacobsen's lab at UCLA). POSIX.
* SISSRs - Site Identification from Short Sequence Reads. BED file input. Raja Jothi @ NIH. Perl.
* QuEST - Quantitative Enrichment of Sequence Tags. Sidow and Myers Labs at Stanford. From the 2008 publication Genome-wide analysis of transcription factor binding sites based on ChIP-Seq data. (C++)
**See also this thread for ChIP-Seq, until I get time to update this list.

Alternate Base Calling

侯补碱基检出
* Rolexa - R-based framework for base calling of Solexa data. Project publication
* Alta-cyclic - "a novel Illumina Genome-Analyzer (Solexa) base caller"

专家评论:(lh3 in sanger)

1. In a commercial package, NCGR uses GMAP (http://www.gene.com/share/gmap/) to alignment Solexa reads. GMAP is free, though.

2. Synamatix has SXOligoSearch (http://synasite.mgrc.com.my:8080/sxo...ligoSearch.php). It is commercial and from the online decription it looks very promising.

3. SOAP (http://soap.genomics.org.cn) by Ruiqiang Li, as has been pointed by ECO.

4. Maq is also able to find SNPs with its own alignment. It has a graphical viewer, but again for its own alignment format.

5. Illumina has a software list: http://www.illumina.com/pagesnrn.ilmn?ID=245. But most of the listed softwares have been quoted here. :-)

6. Anthony Fejes discussed some softwares in his blog (http://www.fejes.ca/labels/DNA.html). May be helpful to someone, too.

7. SSAHA has been optimized for short-reads, too. But yes, SSAHASNP appears in your "SNP/INDEL discovery" category.

8. Ladeana from Gabor's group has recently published a paper on Nature Methods, using their MASAIC and PolyBayesShort.