101. SHOREmap
Extension of the short read analysis pipeline SHORE. SHOREmap supports genome-wide genotyping and candidate-gene sequencing in a single step through analysis of deep sequencing data from a large pool of recombinants.
标签:
102. SSPACE
Stand-alone scaffolder of pre-assembled contigs using paired-read data. SSPACE standard is a stand-alone program for scaffolding pre-assembled contigs using NGS paired-read data.
标签:Genomics
103. CloudBurst
CloudBurst is a parallel read-mapping algorithm optimized for mapping next-generation sequence data to the human genome and other reference genomes.
标签:SNP discovery, Genotyping,Personal genomics
104. Stampy
Uses a hybrid mapping algorithm and a detailed statistical model to achieve both speed and sensitivity, particularly when reads include sequence variation. stampy is a package for mapping short Illumina reads onto a reference genome. It can bs used for genomic resequencing, RNA-Seq a...
标签:
105. MISO
An alternative to Cufflinks, MISO (Mixture-of-Isoforms) is a probabilistic framework that quantitates the expression level of alternatively spliced genes.
标签:RNA-Seq Quantitation, RNA-Seq
106. SHRAP
A sequencing protocol and assembly methodology that utilizes high-throughput short-read technologies.
标签:De-novo assembly
107. MapSplice
We introduce a second generation splice detection algorithm, MapSplice, whose focus is high sensitivity and specificity in the detection of splices as well as CPU and memory efficiency. MapSplice can be applied to both short (<75 bp) and long reads (75 bp). MapSplice is not dependent...
标签:RNA-Seq Alignment
108. SNVMix
Detects single nucleotide variants from next generation sequencing data.
标签:SNP discovery
109. ChromaSig
An unsupervised learning method, which finds, in an unbiased fashion, commonly occurring chromatin signatures in both tiling microarray and sequencing data.
标签:ChIP-on-chip
110. CASHX
Parse, map, quantify and manage large quantities of short-read sequence data.
标签:Small RNA transcriptome
111. RazerS
RazerS allows the user to align sequencing reads of arbitrary length using either the Hamming distance or the edit distance. The tool can work either lossless or with a user-defined loss rate at higher speeds.
标签:Mapping, Read alignment
112. Alta-Cyclic
Alta-Cyclic is a Illumina Genome-Analyzer (Solexa) base caller.
标签:
113. MoDIL
Program to detect small indels in next generation sequencing data
标签:Genomics, InDel discovery
114. BaySeq
Identify differential expressed genes
标签:RNA-Seq Quantitation
115. Atlas-SNP2
Atlas-SNP2 is a SNP discovery tool developed for next generation sequencing platforms
标签:SNP discovery
116. Blixem
a graphical blast viewer
标签:Sequence analysis,Phylogenetics, Homology
117. MrsFAST
mrsFAST is a micro-read substitution-only Fast Alignment Search Tool. mrsFAST is a cache-oblivous short read mapper that optimizes cache usage to get higher performance.
标签:Genomics
118. ShortRead
ShortRead is an R/BioConductor package for input, quality assessment, manipulation, and output of high-throughput sequencing data.
标签:
119. Sole-Search
Determines statistically significant peaks from ChIP experiments
标签:ChIP-Seq
120. ALEXA-Seq
Alternative Expression Analysis by massively parallel RNA sequencing
标签:RNA-Seq Quantitation,Alternative Splicing