专业背景：计算机科学 研究方向与兴趣: JavaEE-Web软件开发, 生物信息学, 数据挖掘与机器学习, 智能信息系统 目前工作: 基因组, 转录组, NGS高通量数据分析, 生物数据挖掘, 植物系统发育和比较进化基因组学
ABySS (Assembly By Short Sequences) is a de novo, parallel,
paired-end sequence assembler that is designed for short reads. ALLPATHS-LG is a whole genome shotgun assembler that can generate
high quality genome assemblies using short reads (~100bp) such as those produced
by the new generation of sequencers. The significant difference between ALLPATHS
and traditional assemblers such as Arachne is that ALLPATHS assemblies are not
necessarily linear, but instead are presented in the form of a graph. This graph
representation retains ambiguities, such as those arising from polymorphism,
uncorrected read errors, and unresolved repeats, thereby providing information
that has been absent from previous genome assemblies.
A Modular, Open-Source whole genome assembler. Convert the "Celera ASM" assembly format to the "Consed ACE" or the
"CAF" file format. Scaffolding tool: ordering and orienting contigs by incorporating
additional information about their relative placement along the genome.
CAP3 is a sequence assembly program for DNA sequence
with or without quality values. This is a graphical, interactive tool for inspecting the ACE format
assembly files generated by CAP3 or phrap. Consed allow to visualise, edit and finish sequences assembled with
phrap. Consed is compatible with Newbler, Cross_match, Phrap and PCAP output.
Euler is a new approach to fragment assembly that abandons the
classical "overlap - layout - consensus" paradigm that is used in all currently
available assembly tools. EULER-SR is a program for de novo assembly of reads (from Roche 454
Live Sciences or Illumina/Solexa).
FLASH, Fast Length Adjustment of SHort reads, is a very accurate fast
tool to merge paired-end reads from fragments that are shorter than twice the
length of reads. The extended length of reads has a significant positive impact
on improvement of genome assemblies. 
The GapCloser is designed to close the gaps emerging during the scaffolding process by SOAPdenovo, using the abundant pair relationships of short reads.
KmerGenie estimates the best k-mer length for genome de novo
assembly.
Maq is a software that builds mapping assemblies from short reads generated by
the next-generation sequencing machines. It is particularly designed for
Illumina/Solexa 1G Genetic Analyzer, and has preliminary functions to handle ABI
SOLID data. 
MaSuRCA is whole genome assembly software. It combines the efficiency
of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA
can assemble data sets containing only short reads from Illumina sequencing or a
mixture of short reads and long reads (Sanger, 454)
Whole genome shotgun and EST sequence assembler for Sanger, 454, and Solexa /
Illumina. Newbler is a software package for de novo DNA sequence assembly. It
is designed specifically for assembling sequence data generated by the 454
GS-series of pyrosequencing platforms sold by 454 Life Science, a Roche
diagnostic. Oases is a de novo transcriptome assembler designed to produce
transcripts from short read sequencing technologies, such as Illumina, SOLiD, or
454 in the absence of any genomic assembly. It was developed by Marcel Schulz
(MPI for Molecular Genomics) and Daniel Zerbino (previously at the European
Bioinformatics Institute (EMBL-EBI), now at UC Santa Cruz). 
A new tool OSLay that uses synteny between matching sequences in a
target assembly and a reference assembly to layout the contigs (or scaffolds) in
the target assembly. The tool provides an interactive visualization of the
computed layout and the result can be imported into the assembly editing tool
Consed to support the design of primer pairs for gap-closure. 
PASA, acronym for Program to Assemble Spliced Alignments, is a eukaryotic genome
annotation tool that exploits spliced alignments of expressed transcript
sequences to automatically model gene structures, and to maintain gene structure
annotation consistent with the most recently available experimental sequence
data. PASA also identifies and classifies all splicing variations supported by
the transcript alignments.
The phred software reads DNA sequencing trace files, calls bases, and
assigns a quality value to each called base. Phrap is a program for assembling
shotgun DNA sequence data. 
Parallel genome assemblies for parallel DNA sequencing. Ray is a parallel
software that computes de novo genome assemblies with next-generation
sequencing data. Ray is written in C++ and can run in parallel on numerous
interconnected computers using the message-passing interface (MPI) standard.
SGA is a de novo genome assembler based on the concept of string graphs. The
major goal of SGA is to be very memory efficient, which is achieved by using a
compressed representation of DNA sequence reads. 
ShoRAH is a software package that allows for inference about the
structure of a population from a set of short sequence reads as obtained from
ultra-deep sequencing of a mixed sample. 
SOAPdenovo-Trans is a de novo transcriptome assembler basing
on the SOAPdenovo framework, adapt to alternative splicing and different
expression level among transcripts.The assembler provides a more accurate,
complete and faster way to construct the full-length transcript sets. SSAHA2 (Sequence Search and Alignment by Hashing Algorithm) is a
pairwise sequence alignment program designed for the efficient mapping of
sequencing reads onto genomic reference sequences. 
This package automates clustering and assembly of a large EST/mRNA
dataset. The clustering is performed by a slightly modified version of NCBI's
megablast , and the resulting clusters are then assembled using CAP3
assembly program. TGICL starts with a large multi-FASTA file (and an optional
peer quality values file) and outputs the assembly files as produced by CAP3.
Trans-ABySS is a software pipeline for analyzing ABySS-assembled
contigs from shotgun transcriptome data. The pipeline accepts assemblies that
were generated across a wide range of k values in order to address variable
transcript expression levels. It first filters and merges the multi-k
assemblies, generating a much smaller set of nonredundant contigs. It contains
scripts that map assembled contigs to known transcripts, currently supporting
the Blat contig-to-genome aligner. It identifies novel splicing events like
exon-skipping, novel exons, retained introns, novel introns, and alternative
splicing. Its scripts can also identify candidate gene-fusions,
single-nucleotide variants, insertions, deletions, and inversions. 
VCAKE is a genetic sequence assembler capable of assembling millions
of small nucleotide reads even in the presence of sequencing error. This
software is currently geared towards de novo assembly of Illumina's Solexa
Sequencing data. Velvet is a de novo genomic assembler specially designed for short
read sequencing technologies, such as Solexa or 454, developed by Daniel Zerbino
and Ewan Birney at the European Bioinformatics Institute (EMBL-EBI), near
Cambridge, in the United Kingdom.
wgs (Celera Assembler) is a de novo whole-genome shotgun (WGS) DNA
sequence assembler. 
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