81. RSEM
We present a generative statistical model and associated inference methods that handle read mapping uncertainty in a principled manner. Through simulations parameterized by real RNASeq data, we show that our method is more accurate than previous methods. Our improved accuracy is the res...
标签:RNA-Seq Alignment, RNA-Seq Quantitation
82. VCAKE
De novo assembly of short reads with robust error correction. An improvement on early versions of SSAKE.
标签:De-novo assembly
83. ATAC
ATAC is a computational process for comparative mapping between two genome assemblies, or between two different genomes.
标签:
84. Crossbow
Crossbow is a cloud-computing software tool that combines the aligner BOWTIE and the SNP caller SOAPsnp. Crossbow is a cloud-computing software tool that combines the aligner BOWTIE and the SNP caller SOAPsnp.
标签:SNP discovery
85. G-Mo.R-Seq
G-Mo.R-Se is a method aimed at using RNA-Seq short reads to build de novo gene models.
标签:RNA-Seq Alignment
86. MiRanalyzer
Web-server for identifying and analyzing miRNA in next-gen sequencing experiments
标签:MiRNA
87. SNPSeeker
Identification of SNPs in pooled genomic samples
标签:SNP discovery
88. CNVseq
标签:Copy number estimation
89. FusionSeq
Identifies fusion transcripts from paired end RNA-Seq data.
标签:Fusion transcripts, RNA-Seq,Fusion genes
90. Epigenome
A bioinformatic pipeline that scores epigenetic alterations according to strength and significance and links them to potentially affected genes.
标签:Epigenomics
91. Trans-ABySS
Trans-ABySS is a software package that is designed to analyze ABySS-assembled whole-genome shotgun transcriptome data.
标签:RNA-Seq, SNP discovery, Fusion genes, InDel discovery, Fusion transcripts
92. Ibis
Ibis (Improved base identification system), is an accurate, fast and easy-to-use base caller for the Illumina sequencing system, which significantly reduces the error rate and increases the output of usable reads. Ibis is faster and makes fewer assumptions about chemistry and technology...
标签:Sequencing
93. DiffBind
Differential Binding Analysis of ChIP-Seq peak data Compute differentially bound sites from multiple ChIP-seq experiments using affinity (quantitative) data. Also enables occupancy (overlap) analysis and plotting functions.
标签:ChIP-Seq
94. Bambus
Bambus is a general purpose scaffolder
标签:
95. USeq
Collection of software tools for for both low and high level analysis of next generation, ultra high throughput signature sequencing data from the Solexa, SOLiD, and 454 platforms. Initial emphasis: chIP-seq and RNA-Seq with FDR estimations
标签:ChIP-Seq, RNA-Seq Alignment
96. Dindel
Calls small indels from short-read sequence data
标签:InDel discovery
97. LAST
Short read alignment program incorporating quality scores
标签:Genomics, Comparative genomics
98. SpliceMap
Detects splice junctions from RNA-seq data. This method does not depend on any existing annotation of gene structures and is capable of finding novel splice junctions with high sensitivity and specificity. It can handle long reads (50–100 nt) and can exploit paired-read information to i...
标签:RNA-Seq Alignment
99. SGA
SGA is a de novo assembler designed to assemble large genomes from high coverage short read data.
标签:
100. EagleView genome viewer
EagleView is an information-rich genome assembler viewer with data integration capability.
标签: